eTrack Comprehensive Analysis Report Summary

This run was generated using eTrack version 1.0 performed on 2020-08-30… Thank you for using this pipeline!!

Quick links

• Assembly summary statistics

• SNP-Variant Calling

• Phylogenetic inference

• Antimicrobial Resistance Profiling

• Plasmid Profiling

• Virulence Factor Determination

• Multi-Locus Sequence Typing (MLST)

• Pangenome Analysis

• Insertion sequence characterization (IS)

Assembly summary statistics

Field	Description
SampleID	Name of the sample
TrimReads	Total number of reads after quality filtering
MeanReadLen	Average read length after quality filtering
Contigs	Number of contigs of the draft genome (>200bp)
GenomeLength	Length (bp) of the draft genome
LargestContig	Length (bp) of the largest contig in the genome
N50	Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly
GC-Content	GC content (%) of the draft genome
Depth	Number of times each nucleotide position in the draft genome has a read that aligns to that position

SampleID	TrimReads	MeanReadLen	Contigs	GenomeLength	LargestContig	N50	GC-Content	Depth
Catt-BWE_048B	230174	169	2240	3715684	11806	2090	51.49	10X
Catt-BWE_054A	304450	155	2462	4118917	17419	2172	50.94	11X
Catt-BWE_113B	311660	162	2273	4247867	27842	2521	50.76	11X
Catt-HIM_031B	164526	165	2995	2563559	4310	913	50.70	10X
Catt-HIM_045B	329330	143	3224	3520313	13526	1258	50.51	13X
Catt-HIM_048B	291558	161	2114	3903224	16987	2403	51.43	12X
Catt-HIM_068A	242972	164	2748	3796931	12856	1680	51.55	10X
Catt-HIM_073A	227696	158	3054	3346460	6620	1272	51.13	10X
Catt-HIM_082A1	298778	163	2396	4267109	13284	2407	51.11	11X
Catt-KAT_009_A1	344352	168	1344	4475396	26936	5163	50.85	12X
Catt-KAT_013A1	239918	167	3023	3487810	10159	1366	51.75	11X
Catt-KAT_036B	90360	167	1226	777772	4764	620	50.33	19X
Home-BWE_054A	341966	163	1789	4542485	21516	3592	51.11	12X
Home-HIM_031A	261270	164	2060	4024124	18944	2607	50.99	10X
Home-HIM_032A	218272	168	2605	3838236	9168	1832	50.87	9X
Home-HIM_045A	479548	142	1520	4254672	24612	4234	50.87	16X
Home-HIM_047B	258442	169	1967	4263045	15928	3108	55.96	10X
Home-HIM_048A	318010	165	1299	4336772	27117	4994	50.96	12X
Home-HIM_068B	250506	161	2738	3788525	9060	1681	50.94	10X
Home-HIM_071A	264128	161	2522	4010382	13352	2100	51.08	10X
Home-HIM_072A	229122	170	2430	3863330	13217	1999	51.41	10X
Home-HIM_073B	274600	165	3133	3997463	12594	1533	50.78	11X
Home-HIM_075A	433206	167	790	4565722	45205	9881	50.98	15X
Home-HIM_82A	275378	172	1845	4425285	24299	3473	51.08	10X
Home-KAT_009A	337726	163	2433	4437467	14004	2489	50.88	12X
Home-KAT_013A	228108	170	2879	3740660	12726	1592	51.14	10X
Home-KAT_023A	321126	158	2630	4020724	14588	1950	51.32	12X
Home-KAT_039B	168914	164	2928	2793862	25204	1032	50.24	9X
Hosp-BWE_048	182824	169	3078	3302835	8241	1225	51.05	9X
Hosp-BWE_054	425850	157	1484	4757167	21565	4755	50.80	14X
Hosp-BWE_076	214110	161	3008	3192002	7609	1205	50.81	10X
Hosp-BWE_106	171380	166	3159	2890869	8594	1005	50.82	9X
Hosp-HIM_031	207346	163	2912	3577483	9055	1470	50.70	9X
Hosp-HIM_045	387642	150	1866	4158817	12843	3117	51.01	13X
Hosp-HIM_048	330554	156	2939	4079520	19766	1687	50.22	12X
Hosp-HIM_068	398734	169	833	4556867	40148	8964	50.71	14X
Hosp-HIM_071A	327566	159	2917	4249416	12074	1830	51.03	12X
Hosp-HIM_82	214874	170	2860	3736242	9583	1563	50.97	9X
Hosp-KAT_009	289630	155	2779	3956709	10531	1789	50.83	11X
Hosp-KAT_013	233622	169	2759	3728264	9258	1688	51.03	10X
Hosp-KAT_023	293682	164	2931	4145128	10214	1759	51.09	11X
Hosp-KAT_039	260886	164	2375	4130433	18456	2290	50.99	10X

Select the parameter

Number of reads

## Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
## Please use `arrange()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.

Average number of reads per sample = 277971

Average read length

Average read length per sample = 163 bp

Number of contigs

Average number of contigs per sample = 2394

Genome length

Average genome length per sample = 3847275 bp

Largest contig length

Average largest contig length per sample = 15857 bp

N50

Average N50 per sample = 2531 bp

GC content

Average GC content per sample = 51.077%

Sequencing depth

Average sequencing depth = 11.214X

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Phylogenetic inference

Phylogenetic inference based on vcf SNPS

Rectangular (phylogram)

Circular (phylogram)

Rectangular (cladogram)

Circular (cladogram)

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Antimicrobial Resistance Profiling

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Gaps	Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product
Resistance	Antibiotic that the gene confers resistance to

Select the samples and the database

Catt-BWE_048B

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00153	739	1542	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig01204	109	969	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig01222	42	551	dfrA8_1	0/0	100	100.0	U10186	dfrA8	Trimethoprim
contig00153	1603	2418	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00594	740	1945	tet(B)_2	0/0	100	99.9	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00933	197	1354	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00153	739	1542	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig01074	92	911	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00996	681	1372	baeR	0/0	95.7	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00003	7704	9074	cpxA	0/0	99.8	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00490	620	1252	CRP	0/0	100.0	99.5	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01222	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig01021	105	1277	emrA	0/0	100.0	98.3	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00659	705	1037	Escherichia_coli_emrE	0/0	100.0	92.5	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00810	81	494	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00160	27	410	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00186	1236	2393	mdtE	0/0	100.0	99.6	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00503	331	1557	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00134	1897	3129	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00534	359	1390	mdtN	0/0	100.0	98.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00698	54	1520	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00310	945	1421	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig01265	217	1139	pmrF	0/0	95.2	99.3	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00153	1603	2418	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig01204	109	969	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00594	740	1945	tet(B)	0/0	100.0	99.7	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00153	739	1542	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig01204	109	969	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00153	1603	2418	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00594	740	1945	(Tet)tetB	0/0	100	99.6	AB089594:1-1206	(Tet)tetB	NA
contig01222	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00153	739	1542	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig01204	109	969	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00153	1603	2418	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00594	740	1945	(Tet)tetB	0/0	100	99.6	AB089594:1-1206	(Tet)tetB	NA
contig01222	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00933	197	1354	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00153	739	1566	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig01074	92	911	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00996	681	1372	BAER	0/0	95.7	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00003	7009	7707	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00003	7704	9074	CPXAR	0/0	99.8	99.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00490	620	1252	CRP	0/0	100.0	99.5	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01222	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig01021	105	1277	EMRA	0/0	100.0	98.3	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00810	81	494	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00160	27	416	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00160	430	864	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00186	1236	2393	MDTE	0/0	100.0	99.6	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00503	331	1557	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00134	1897	3129	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00534	359	1390	MDTN	0/0	100.0	98.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00698	54	1520	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00310	945	1421	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00659	705	1037	MVRC	0/0	100.0	92.5	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig01265	217	1139	PMRF	0/0	95.2	99.3	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00025	230	1099	ROBA	0/0	100.0	99.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00734	1383	1706	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00153	1603	2418	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00594	740	1945	TETB	0/0	100.0	99.9	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA

Catt-BWE_054A

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00329	1	2891	acrB	0/0	91.8	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00676	1136	1798	acrS	0/0	100.0	97.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00955	1	805	bacA	0/0	97.9	96.8	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00107	3712	4433	baeR	0/0	99.9	98.2	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00107	2312	3715	baeS	0/0	100.0	97.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00069	3582	4955	cpxA	0/0	100.0	98.2	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00179	2848	3480	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00099	2017	3072	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01097	478	1008	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00099	479	2017	emrY	0/0	100.0	97.6	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00038	447	2090	eptA	0/0	100.0	98.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00152	2583	3776	Escherichia_coli_acrA	0/0	100.0	98.9	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00087	942	2075	Escherichia_coli_ampC	0/0	100.0	96.9	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00557	850	1182	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00099	3596	4210	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00103	1549	2277	gadW	0/0	100.0	95.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00103	356	1180	gadX	0/0	100.0	96.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00287	666	1079	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00278	1003	1386	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00251	1077	2231	mdtE	1/3	99.7	98.3	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00371	343	1374	mdtN	0/0	100.0	97.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00170	2048	3016	pmrF	0/0	100.0	98.3	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	942	2075	(Bla)AmpC2_Ecoli	0/0	100	96.9	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00315	839	2740	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	942	2075	(Bla)AmpC2_Ecoli	0/0	100	96.9	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00315	839	2740	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00152	2583	3776	ACRA	0/0	100.0	98.9	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00329	1	2891	ACRB	0/0	91.8	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00676	1136	1798	ACRS	0/0	100.0	97.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00955	1	805	BACA	0/0	97.9	97.0	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00107	3712	4433	BAER	0/0	99.9	98.2	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00107	2312	3715	BAES	0/0	100.0	97.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00087	942	2075	BLAEC	0/0	100.0	97.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00069	2887	3585	CPXAR	0/0	100.0	99.3	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00069	3582	4955	CPXAR	0/0	100.0	98.2	MEG_2119	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00179	2848	3480	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00021	4410	5600	EMRD	0/0	100.0	98.1	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00099	2017	3180	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01097	478	1008	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00099	479	2017	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00038	447	2090	EPTA	0/0	100.0	98.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00103	1549	2277	GADW	0/0	100.0	97.4	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00103	356	1180	GADX	0/0	100.0	96.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00287	666	1079	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00278	997	1386	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00278	548	982	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00251	1077	2231	MDTE	1/3	99.7	98.3	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00995	730	1059	MDTI	0/0	100.0	98.5	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00995	378	743	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00371	343	1374	MDTN	0/0	100.0	97.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00557	850	1182	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00315	839	2740	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00170	2048	3016	PMRF	0/0	100.0	98.3	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00841	699	1568	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA

Catt-BWE_113B

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00321	175	3159	acrF	0/0	96.1	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00254	2788	3450	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00783	1026	1845	bacA	0/0	99.8	98.8	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00521	1687	2319	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00290	843	2381	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig01013	320	1375	emrK	0/0	100.0	98.4	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00537	300	830	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00035	4331	5524	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00052	1444	2748	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig01428	296	910	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00013	1225	1953	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00013	33	857	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00470	878	1291	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00280	2502	2885	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00125	3296	4543	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00125	174	3296	mdtB	0/0	100.0	98.4	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00013	5454	6611	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00013	2316	5429	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00374	972	2198	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00383	1246	2478	mdtM	0/0	100.0	96.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00171	1319	1793	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00466	1479	2645	ugd	0/0	100.0	97.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00522	795	2438	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00052	1444	2748	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00698	249	2058	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	95.2	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

NCBI

## [1] "No antibiotic resitance genes from NCBI database were found"

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00035	4331	5524	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00321	175	3159	ACRF	0/0	96.1	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00254	2788	3450	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00222	1927	3779	ASMA	0/0	100.0	98.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00783	1026	1845	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00061	3007	4197	BCR	0/0	100.0	98.1	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig01188	224	922	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00521	1687	2319	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00290	843	2381	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig01013	320	1483	EMRK	0/0	100.0	98.5	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00537	300	830	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00013	1225	1953	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00013	33	857	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00470	878	1291	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00280	2496	2885	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00280	2048	2482	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00125	3296	4543	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00125	174	3296	MDTB	0/0	100.0	98.4	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00013	5454	6611	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00013	2316	5429	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00374	972	2198	MDTG	0/0	100.0	99.4	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00405	1992	2321	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00405	2308	2673	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00461	701	2074	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00383	1246	2478	MDTM	0/0	100.0	96.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00171	1319	1793	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00698	249	2058	PBP2	0/0	95.2	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00052	1444	2748	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00928	454	1323	ROBA	0/0	100.0	99.4	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00466	1479	2645	UGD	0/0	100.0	97.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00522	795	2438	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Catt-HIM_031B

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00117	199	1371	emrA	0/0	100	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig01192	8	622	evgA	0/0	100	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline

ARG-ANNOT

## [1] "No antibiotic resitance genes from ARG-ANNOT database were found"

NCBI

## [1] "No antibiotic resitance genes from NCBI database were found"

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00533	363	1061	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00117	199	1371	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig01276	412	759	QACEDELTA1	0/0	100.0	100.0	MEG_5829	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACEDELTA1	NA
contig00477	420	1206	ROBA	0/0	90.5	99.5	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA

Catt-HIM_045B

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00351	679	1884	tet(B)_1	0/0	100	100	AP000342	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00159	5	1060	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00236	126	1769	eptA	0/0	100.0	99.5	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00622	1	1074	Escherichia_coli_ampC	0/0	94.7	97.4	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig02078	103	435	Escherichia_coli_emrE	0/0	100.0	97.6	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00159	1584	2198	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00021	1423	2151	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00021	231	1055	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00172	567	1793	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig01539	368	844	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00711	125	1093	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00351	679	1884	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00622	1	1074	(Bla)AmpC2_Ecoli	0/0	94.7	97.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00351	679	1884	(Tet)tetB	0/0	100.0	99.8	AB089594:1-1206	(Tet)tetB	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00622	1	1074	(Bla)AmpC2_Ecoli	0/0	94.7	97.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00351	679	1884	(Tet)tetB	0/0	100.0	99.8	AB089594:1-1206	(Tet)tetB	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00622	1	1074	BLAEC	0/0	94.7	99.9	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig01032	1	670	CPXAR	0/0	95.8	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00560	198	1388	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00159	5	1168	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00236	126	1769	EPTA	0/0	100.0	99.5	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00021	1423	2151	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00021	231	1055	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01348	386	820	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00172	567	1793	MDTG	0/0	100.0	99.4	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig01539	368	844	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig02078	103	435	MVRC	0/0	100.0	97.6	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00711	125	1093	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00111	522	845	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00351	679	1884	TETB	0/0	100.0	100.0	MEG_7042	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA

Catt-HIM_048B

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00971	1	1180	mdf(A)_1	0/0	95.7	99.9	Y08743	mdf(A)
contig00899	23	679	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00452	372	1187	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00196	509	3613	acrF	0/0	100.0	99.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig01301	227	1048	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00682	477	1199	baeR	0/0	100.0	99.9	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00123	3055	4428	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00129	1004	1636	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00139	2800	3855	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01931	52	582	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00139	1262	2800	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00192	103	1746	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00198	1147	2340	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00021	3558	4691	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00971	2	1180	Escherichia_coli_mdfA	0/0	95.6	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig01673	1	577	evgA	0/0	93.8	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig01290	1	817	gadX	0/0	99.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00029	1150	1563	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig01291	568	951	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00532	138	1385	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00257	1306	2514	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00747	305	1771	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00422	1644	2118	mphB	0/0	99.6	97.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00330	836	1804	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00899	23	679	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00452	372	1187	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00748	383	1850	tolC	0/0	98.7	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	3558	4691	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00100	592	2493	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00899	23	679	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00452	372	1187	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	3558	4691	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00100	592	2493	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00899	23	679	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00452	372	1187	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00198	1147	2340	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00196	509	3613	ACRF	0/0	100.0	99.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00496	542	2394	ASMA	0/0	100.0	98.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig01301	227	1048	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00682	477	1199	BAER	0/0	100.0	99.9	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00133	56	1246	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00021	3558	4691	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00123	2360	3058	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00123	3055	4428	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00129	1004	1636	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00429	1513	2593	EMRD	0/0	90.8	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00139	2800	3963	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01931	52	582	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00139	1262	2800	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00192	103	1746	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01290	1	817	GADX	0/0	99.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00029	1150	1563	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig01291	562	951	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig01291	113	547	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00971	1	1180	MDFA	0/0	95.7	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00532	138	1385	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00257	1306	2514	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00747	305	1771	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00422	1644	2118	MPHB	0/0	99.6	97.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00100	592	2493	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00330	836	1804	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00899	23	679	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig01419	187	977	ROBA	0/0	90.9	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig01532	543	865	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00452	372	1187	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Catt-HIM_068A

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00824	739	1461	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00342	532	1164	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01111	1	1103	emrA	0/0	94.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig01026	688	1218	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00076	110	1753	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00265	426	1619	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig01869	1	555	evgA	0/0	90.2	98.9	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00462	252	980	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01649	1	824	gadX	0/0	99.9	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00647	1294	1707	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00627	266	1423	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00301	395	1426	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00176	1	1397	mdtP	0/0	95.2	98.1	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00018	2040	3788	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00012	1192	2679	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig01151	78	1211	ugd	0/0	97.2	96.3	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

## [1] "No antibiotic resitance genes from ARG-ANNOT database were found"

NCBI

## [1] "No antibiotic resitance genes from NCBI database were found"

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00265	426	1619	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00202	1174	2950	ASMA	0/0	95.8	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00824	739	1461	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00342	532	1164	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01111	1	1103	EMRA	0/0	94.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig01026	688	1218	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00076	110	1753	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00462	252	980	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01649	1	824	GADX	0/0	99.9	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00647	1294	1707	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00627	266	1423	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig02220	96	461	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00301	395	1426	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00176	1	1397	MDTP	0/0	95.2	98.1	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00018	2040	3788	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00166	1083	1952	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00313	2025	2347	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig01151	78	1211	UGD	0/0	97.2	96.3	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

Catt-HIM_073A

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00691	197	1354	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00625	1	1400	baeS	0/0	99.7	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00034	999	1631	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00404	758	1778	emrK	0/0	96.7	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00068	564	1094	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00210	168	1811	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00265	7	1140	Escherichia_coli_ampC	0/0	100.0	97.4	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00328	259	987	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01598	1	772	gadX	0/0	93.6	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00646	1019	1402	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00472	1	1187	mdtG	0/0	96.7	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00397	1302	1776	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00051	960	2708	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00197	270	1757	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00265	7	1140	(Bla)AmpC2_Ecoli	0/0	100	97.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00265	7	1140	(Bla)AmpC2_Ecoli	0/0	100	97.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00691	197	1354	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00625	1	1400	BAES	0/0	99.7	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00265	7	1140	BLAEC	0/0	100.0	98.1	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00534	213	911	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00034	999	1631	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00068	564	1094	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00210	168	1811	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00328	259	987	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01598	1	772	GADX	0/0	93.6	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00646	1013	1402	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00646	565	999	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00472	1	1187	MDTG	0/0	96.7	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig01908	97	462	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00397	1302	1776	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00051	960	2708	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA

Catt-HIM_082A1

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00056	5239	5901	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00158	84	806	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00158	803	2206	baeS	0/0	100.0	98.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00053	2156	2788	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00529	4	1176	emrA	0/0	100.0	98.3	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00755	672	1727	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00855	397	1590	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	8147	9280	Escherichia_coli_ampC	0/0	100.0	97.6	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00407	1213	2370	Escherichia_coli_ampH	0/0	100.0	98.6	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00991	1249	1581	Escherichia_coli_emrE	0/0	100.0	99.4	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01513	25	639	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig01296	1	823	gadX	0/0	99.8	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00657	62	475	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00085	3515	3898	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00324	215	1462	mdtA	0/0	100.0	98.1	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00125	964	4077	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00184	651	1877	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00364	1266	2474	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00357	1174	2406	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00397	387	1418	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00511	602	2068	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00686	1	964	pmrF	0/0	99.5	99.2	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig01319	72	1195	ugd	0/0	96.3	96.3	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	8147	9280	(Bla)AmpC2_Ecoli	0/0	100	97.6	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00407	1213	2370	(Bla)ampH_Ecoli	0/0	100	98.6	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	8147	9280	(Bla)AmpC2_Ecoli	0/0	100	97.6	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00407	1213	2370	(Bla)ampH_Ecoli	0/0	100	98.6	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00855	397	1590	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00056	5239	5901	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00407	1213	2370	AMPH	0/0	100.0	98.6	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00679	273	2125	ASMA	0/0	100.0	98.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00158	84	806	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00158	803	2206	BAES	0/0	100.0	98.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00007	8147	9280	BLAEC	0/0	100.0	99.3	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00053	2156	2788	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00529	4	1176	EMRA	0/0	100.0	98.3	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00755	672	1835	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01296	1	823	GADX	0/0	99.8	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00657	62	475	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00085	3509	3898	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00085	3061	3495	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00324	215	1462	MDTA	0/0	100.0	98.1	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00125	964	4077	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00184	651	1877	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00364	1266	2474	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00550	497	826	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00550	813	1178	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00357	1174	2406	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00397	387	1418	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00511	602	2068	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00991	1249	1581	MVRC	0/0	100.0	99.4	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00686	1	964	PMRF	0/0	99.5	99.2	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00035	5429	6298	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00172	2869	3191	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig01319	72	1195	UGD	0/0	96.3	96.3	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

Catt-KAT_009_A1

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00417	1201	2004	aph(3’’)-Ib_5	0/0	100.0	99.9	AF321551	aph(3’’)-Ib	Streptomycin
contig00417	365	1201	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig01129	1	812	blaOXA-1_1	0/0	97.7	99.9	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig01025	17	877	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig01005	42	551	dfrA8_1	0/0	100.0	100.0	U10186	dfrA8	Trimethoprim
contig00173	4671	5903	mdf(A)_1	0/0	100.0	98.9	Y08743	mdf(A)
contig00417	2065	2880	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00557	1439	2644	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00189	3062	6211	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00103	6882	8039	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00103	3766	6870	acrF	0/0	100.0	99.1	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00454	2689	3351	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00417	1201	2004	APH(3’’)-Ib	0/0	100.0	99.6	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00417	365	1201	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00756	1082	1903	bacA	0/0	100.0	99.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00426	764	1486	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00658	943	2316	cpxA	0/0	100.0	98.1	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00436	719	1351	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01005	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00206	880	2418	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00008	2550	3605	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00847	684	1214	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00008	1012	2550	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00054	2406	4049	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00189	1846	3039	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00020	9353	10486	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00883	144	1448	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00261	1222	2379	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00173	4671	5903	Escherichia_coli_mdfA	0/0	100.0	97.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00008	4129	4743	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	4748	8341	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00317	1586	2314	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00317	394	1218	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00766	215	1462	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00136	2008	5085	mdtC	0/0	100.0	97.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00325	1236	2393	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00562	772	1998	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00190	1	1204	mdtM	0/0	97.7	95.6	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00159	4593	6644	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00159	3130	4596	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00080	5870	6346	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig01129	1	812	OXA-1	0/0	97.7	99.9	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00546	668	1636	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00417	2065	2880	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig01025	17	877	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00557	1439	2644	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00013	12612	14099	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00262	1512	2678	ugd	0/0	100.0	98.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00550	1286	2792	yojI	0/0	91.7	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01066	112	916	(AGly)aadA1-pm	0/0	96.9	99.6	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00417	1201	2004	(AGly)strA	0/0	100.0	99.8	AB366441:22458-23261	(AGly)strA	NA
contig00417	365	1201	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00883	144	1448	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00020	9353	10486	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00261	1222	2379	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01129	1	812	(Bla)blaOXA-1	0/0	97.7	99.9	JQ682867:1-831	(Bla)blaOXA-1	NA
contig01025	17	877	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00307	1513	3414	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00417	2065	2880	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00557	1439	2644	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig01005	42	551	(Tmt)dfrA8	0/0	100.0	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01066	112	916	(AGly)aadA1-pm	0/0	96.9	99.6	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00417	1201	2004	(AGly)strA	0/0	100.0	99.8	AB366441:22458-23261	(AGly)strA	NA
contig00417	365	1201	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00883	144	1448	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00020	9353	10486	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00261	1222	2379	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01129	1	812	(Bla)blaOXA-1	0/0	97.7	99.9	JQ682867:1-831	(Bla)blaOXA-1	NA
contig01025	17	877	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00307	1513	3414	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00417	2065	2880	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00557	1439	2644	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig01005	42	551	(Tmt)dfrA8	0/0	100.0	100.0	U10186:711-1220	(Tmt)dfrA8	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00189	1846	3039	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00189	3062	6211	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00103	6882	8039	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00103	3766	6870	ACRF	0/0	100.0	99.1	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00454	2689	3351	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00261	1222	2379	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig01066	112	916	ANT3-DPRIME	0/0	96.9	99.6	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00417	1201	2028	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00417	365	1201	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00397	2008	3860	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00756	1082	1903	BACA	0/0	100.0	99.0	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00426	764	1486	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00483	1197	2387	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00020	9353	10486	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00658	248	946	CPXAR	0/0	100.0	99.6	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00658	943	2316	CPXAR	0/0	100.0	98.1	MEG_2119	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00436	719	1351	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01005	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00206	880	2418	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00009	174	1364	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00008	2550	3713	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00847	684	1214	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00008	1012	2550	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00054	2406	4049	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00008	4748	8341	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00317	1586	2314	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00317	394	1218	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00216	587	1021	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00173	4671	5903	MDFA	0/0	100.0	99.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00766	215	1462	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00136	2008	5085	MDTC	0/0	100.0	97.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00325	1236	2393	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00562	772	1998	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00495	2704	3033	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00495	2352	2717	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00190	1	1204	MDTM	0/0	97.7	95.6	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00159	4593	6644	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00159	3130	4596	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00080	5870	6346	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig01129	1	812	OXA	0/0	97.7	99.9	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00307	1513	3414	PBP2	0/0	100.0	99.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00883	144	1448	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00546	668	1636	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00044	9120	9989	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00004	14455	14778	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00417	2065	2880	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00557	1439	2644	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00262	1512	2678	UGD	0/0	100.0	98.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00550	1286	2792	YOGI	0/0	91.7	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Catt-KAT_013A1

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01264	164	983	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00132	1565	2938	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00118	2456	3059	CRP	0/0	95.4	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00662	1	1489	eptA	0/0	90.6	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00382	529	1722	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00158	687	1820	Escherichia_coli_ampC	0/0	100.0	97.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00589	1	332	Escherichia_coli_emrE	0/0	99.7	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01009	44	772	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01912	220	603	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00843	109	1266	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00454	329	1360	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00158	687	1820	(Bla)AmpC2_Ecoli	0/0	100	97.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00158	687	1820	(Bla)AmpC2_Ecoli	0/0	100	97.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00382	529	1722	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig01264	164	983	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00158	687	1820	BLAEC	0/0	100.0	98.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00132	870	1568	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00132	1565	2938	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00118	2456	3059	CRP	0/0	95.4	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00662	1	1489	EPTA	0/0	90.6	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01009	44	772	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01912	214	603	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00843	109	1266	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00454	329	1360	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00589	1	332	MVRC	0/0	99.7	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00742	92	961	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig01388	533	856	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA

Catt-KAT_036B

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00015	366	1190	gadX	0/0	100	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam

ARG-ANNOT

## [1] "No antibiotic resitance genes from ARG-ANNOT database were found"

NCBI

## [1] "No antibiotic resitance genes from NCBI database were found"

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00015	366	1190	GADX	0/0	100	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA

Home-BWE_054A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00947	844	1647	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00947	8	844	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig01185	1	792	blaTEM-104_1	0/0	92.0	100.0	AF516719	blaTEM-104
contig00280	940	1599	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00019	2913	4145	mdf(A)_1	0/0	100.0	98.0	Y08743	mdf(A)
contig00689	928	2174	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01002	197	1354	acrE	0/0	100.0	98.3	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00401	2775	3437	acrS	0/0	100.0	97.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00947	844	1647	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00947	8	844	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00172	283	1102	bacA	0/0	99.8	96.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00833	261	1664	baeS	0/0	100.0	97.1	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00280	940	1599	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00950	277	1650	cpxA	0/0	100.0	98.3	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00408	2162	2794	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00444	219	1391	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00432	2298	3305	emrK	0/0	95.5	97.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00444	1518	2048	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00432	760	2298	emrY	0/0	100.0	97.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00277	2397	4040	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00359	2308	3501	Escherichia_coli_acrA	0/0	100.0	98.9	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00092	2723	3856	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00112	5016	6173	Escherichia_coli_ampH	0/0	100.0	96.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00019	2913	4145	Escherichia_coli_mdfA	0/0	100.0	96.5	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig01110	329	943	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00283	1403	2131	gadW	0/0	100.0	95.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00283	210	1034	gadX	0/0	100.0	96.6	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00628	270	683	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00205	1	673	kdpE	0/0	99.3	96.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00033	8217	8600	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00671	154	1401	mdtA	0/0	100.0	97.1	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00144	739	3816	mdtC	0/0	100.0	96.3	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00835	1	1214	mdtG	0/0	98.9	98.6	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00262	1291	2499	mdtH	0/0	100.0	98.2	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00180	2664	3896	mdtM	0/0	100.0	97.1	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00478	666	2717	mdtO	0/0	100.0	97.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00155	1199	1673	mphB	0/0	99.6	96.0	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00257	1820	2788	pmrF	0/0	100.0	98.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig01185	1	792	TEM-104	0/0	92.0	100.0	AF516719:214-1075	TEM-104 is a beta-lactamase found in Klebsiella pneumoniae.	cephalosporin, monobactam, penam, penem
contig00689	928	2174	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00008	9704	11191	tolC	0/0	100.0	98.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00440	78	1244	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00947	844	1647	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00947	8	844	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00092	2723	3856	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00112	5016	6173	(Bla)ampH_Ecoli	0/0	100	96.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01185	1	792	(Bla)blaTEM-104	0/0	92	100.0	AF516719:215-1075	(Bla)blaTEM-104	NA
contig00029	5460	7361	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00280	940	1599	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00689	900	2174	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00947	844	1647	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00947	8	844	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00092	2723	3856	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00112	5016	6173	(Bla)ampH_Ecoli	0/0	100	96.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01185	1	792	(Bla)blaTEM-104	0/0	92	100.0	AF516719:215-1075	(Bla)blaTEM-104	NA
contig00029	5460	7361	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00280	940	1599	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00689	900	2174	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00359	2308	3501	ACRA	0/0	100.0	98.9	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig01002	197	1354	ACRE	0/0	100.0	98.3	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00401	2775	3437	ACRS	0/0	100.0	97.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00112	5016	6173	AMPH	0/0	100.0	96.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00947	844	1669	APH3-DPRIME	0/0	99.8	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00947	8	844	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00249	2511	4363	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00172	283	1102	BACA	0/0	99.8	97.0	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00833	261	1664	BAES	0/0	100.0	97.1	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00427	452	1642	BCR	0/0	100.0	96.1	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00092	2723	3856	BLAEC	0/0	100.0	98.5	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00280	929	1599	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00950	277	1650	CPXAR	0/0	100.0	98.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00408	2162	2794	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00444	219	1391	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00738	1101	2216	EMRD	0/0	93.7	97.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00444	1518	2048	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00432	760	2298	EMRY	0/0	100.0	97.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00277	2397	4040	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00283	1403	2131	GADW	0/0	100.0	97.5	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00283	210	1034	GADX	0/0	100.0	96.6	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00628	270	683	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00205	1	673	KDPE	0/0	99.3	96.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00033	8217	8606	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00033	8621	9055	MARR	0/0	100.0	98.6	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00019	2913	4145	MDFA	0/0	100.0	98.1	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00671	154	1401	MDTA	0/0	100.0	97.1	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00144	739	3816	MDTC	0/0	100.0	96.3	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00835	1	1214	MDTG	0/0	98.9	99.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00262	1291	2499	MDTH	0/0	100.0	98.2	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00461	147	512	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00180	2664	3896	MDTM	0/0	100.0	97.1	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00478	666	2717	MDTO	0/0	100.0	97.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00155	1199	1673	MPHB	0/0	99.6	96.0	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00029	5460	7361	PBP2	0/0	100.0	98.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00257	1820	2788	PMRF	0/0	100.0	98.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig01147	128	997	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00616	592	914	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig01185	1	1159	TEM	0/0	91.4	99.3	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00689	900	2174	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00440	78	1244	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

Home-HIM_031A

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	3553	6702	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig01295	392	1054	acrS	0/0	100.0	99.2	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00060	2465	3187	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00060	1065	2468	baeS	0/0	100.0	98.2	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00121	3577	4950	cpxA	0/0	100.0	98.7	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00244	2146	2778	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00305	1508	2680	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00422	1046	2101	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00305	851	1381	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00034	2337	3530	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00242	1846	2979	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00116	1096	2400	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00047	1816	2973	Escherichia_coli_ampH	0/0	100.0	99.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00167	1454	2182	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00167	262	1086	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01572	88	471	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00546	215	1462	mdtA	0/0	100.0	98.3	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00609	927	2084	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00663	1	1225	mdtM	0/0	99.3	95.8	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00093	2615	4081	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig01899	1	433	mphB	0/0	90.8	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00719	485	1453	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00020	3295	4782	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00270	1	1628	yojI	0/0	99.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00116	1096	2400	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00242	1846	2979	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00047	1816	2973	(Bla)ampH_Ecoli	0/0	100	99.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00116	1096	2400	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00242	1846	2979	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00047	1816	2973	(Bla)ampH_Ecoli	0/0	100	99.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	2337	3530	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00034	3553	6702	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig01295	392	1054	ACRS	0/0	100.0	99.2	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00047	1816	2973	AMPH	0/0	100.0	99.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00060	2465	3187	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00060	1065	2468	BAES	0/0	100.0	98.2	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00242	1846	2979	BLAEC	0/0	100.0	99.9	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00121	2882	3580	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00121	3577	4950	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00244	2146	2778	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00305	1508	2680	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00029	6037	7227	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00422	1046	2209	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00305	851	1381	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00167	1454	2182	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00167	262	1086	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01572	82	471	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00546	215	1462	MDTA	0/0	100.0	98.3	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00609	927	2084	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig01239	635	1000	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00339	1719	3092	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00663	1	1225	MDTM	0/0	99.3	95.8	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00093	2615	4081	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig01899	1	433	MPHB	0/0	90.8	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00116	1096	2400	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00719	485	1453	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00419	694	1563	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00066	578	901	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00270	1	1628	YOGI	0/0	99.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Home-HIM_032A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00604	556	1359	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig01209	6	866	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00125	1789	2262	dfrA1_10	0/0	100	99.8	AF203818	dfrA1	Trimethoprim

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00604	556	1359	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00336	1127	2500	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00157	1034	1666	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00125	1789	2262	dfrA1	0/0	100.0	100.0	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00063	1557	2612	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01134	185	715	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00063	19	1557	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00013	2483	4126	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00308	661	1854	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00435	940	2073	Escherichia_coli_ampC	0/0	100.0	98.4	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00003	2617	3774	Escherichia_coli_ampH	0/0	100.0	99.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig01004	731	1063	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00063	3136	3750	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00200	514	1242	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig02459	57	470	H-NS	0/0	100.0	99.8	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00592	1	1131	mdtA	0/0	90.6	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00243	1226	2383	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00352	509	1735	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00284	17	1483	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00466	1299	1775	mphB	0/0	100.0	99.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig01209	6	866	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00006	5960	7447	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00125	905	1706	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00604	556	1359	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00435	940	2073	(Bla)AmpC2_Ecoli	0/0	100.0	98.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	2617	3774	(Bla)ampH_Ecoli	0/0	100.0	99.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01209	6	866	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig01090	172	822	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00125	1789	2262	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00125	905	1706	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00604	556	1359	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00435	940	2073	(Bla)AmpC2_Ecoli	0/0	100.0	98.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	2617	3774	(Bla)ampH_Ecoli	0/0	100.0	99.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01209	6	866	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig01090	172	822	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00125	1789	2262	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00308	661	1854	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00003	2617	3774	AMPH	0/0	100.0	99.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00125	905	1706	ANT3-DPRIME	0/0	96.5	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00604	556	1383	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00651	1	1833	ASMA	0/0	98.9	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00435	940	2073	BLAEC	0/0	100.0	99.9	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00336	432	1130	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00336	1127	2500	CPXAR	0/0	100.0	99.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00157	1034	1666	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00125	1789	2262	DFRA	0/0	100.0	99.8	MEG_2528	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00295	910	2100	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00063	1557	2720	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01134	185	715	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00063	19	1557	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00013	2483	4126	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00200	514	1242	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig02459	57	470	HNS	0/0	100.0	99.8	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00592	1	1131	MDTA	0/0	90.6	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00243	1226	2383	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00352	509	1735	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig02004	260	625	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00284	17	1483	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00466	1299	1775	MPHB	0/0	100.0	99.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig01004	731	1063	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00373	1362	2231	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00042	1559	1882	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig01209	1	1229	TEM	0/0	96.9	99.3	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA

Home-HIM_045A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00440	1392	2624	mdf(A)_1	0/0	100	98.5	Y08743	mdf(A)	NA

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00472	1	2919	acrB	0/0	92.7	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00935	197	1354	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00085	4435	7308	acrF	0/0	92.6	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00247	4126	4788	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00333	2481	3884	baeS	0/0	100.0	99.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00240	3587	4960	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00362	2156	2788	CRP	0/0	100.0	99.5	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00184	3493	5031	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00886	662	1652	emrK	0/0	93.8	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01004	228	758	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00061	2495	4138	eptA	0/0	100.0	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00364	2318	3511	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	7469	8602	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00026	5757	6914	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00565	1362	1694	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00440	1392	2624	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00165	364	978	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00165	983	4576	evgS	0/0	100.0	98.9	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00370	725	1453	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00154	5416	5829	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig01198	309	943	kdpE	0/0	93.7	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00357	2066	2449	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00412	1236	2393	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00122	4636	5862	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00072	3426	4634	mdtH	0/0	100.0	98.6	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00016	821	2053	mdtM	0/0	100.0	96.1	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00027	8561	10612	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00027	7098	8564	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00201	289	765	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00052	6132	7100	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00058	376	1863	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00371	108	1751	yojI	0/0	100.0	98.5	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00022	7469	8602	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00026	5757	6914	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00022	7469	8602	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00026	5757	6914	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00364	2318	3511	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00472	1	2919	ACRB	0/0	92.7	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00935	197	1354	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00085	4435	7308	ACRF	0/0	92.6	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00247	4126	4788	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00026	5757	6914	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00564	865	2689	ASMA	0/0	98.4	96.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00333	2481	3884	BAES	0/0	100.0	99.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00022	7469	8602	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00240	2892	3590	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00240	3587	4960	CPXAR	0/0	100.0	99.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00362	2156	2788	CRP	0/0	100.0	99.5	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00184	3493	5031	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00226	3772	4962	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig01004	228	758	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00061	2495	4138	EPTA	0/0	100.0	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00165	983	4576	EVGS	0/0	100.0	98.9	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00370	725	1453	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00154	5416	5829	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig01198	309	943	KDPE	0/0	93.7	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00357	2060	2449	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00357	1612	2046	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00440	1392	2624	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00412	1236	2393	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00122	4636	5862	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00072	3426	4634	MDTH	0/0	100.0	98.6	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00016	821	2053	MDTM	0/0	100.0	96.1	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00027	8561	10612	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00027	7098	8564	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00201	289	765	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00565	1362	1694	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00052	6132	7100	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00062	5976	6845	ROBA	0/0	100.0	99.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00010	5613	5936	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00371	108	1751	YOGI	0/0	100.0	98.5	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Home-HIM_047B

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00667	1332	1757	fosA_7	0/0	100	96.5	AEXB01000013	fosA	Fosfomycin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00588	1053	2246	Enterobacter_cloacae_acrA	0/0	100	94.9	DQ679966:299-1493	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00667	1332	1757	FosA2	0/0	100	92.0	EU487198:216-642	An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.	fosfomycin

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00667	1332	1757	(Fcyn)FosA2	0/0	100	92	EU487198:217-642	(Fcyn)FosA2	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00667	1332	1757	(Fcyn)FosA2	0/0	100	92	EU487198:217-642	(Fcyn)FosA2	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00588	1053	2246	ACRB	0/0	100.0	94.9	MEG_402	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00488	1757	2816	ACT	0/0	92.5	99.1	MEG_439	Drugs:betalactams:Class_C_betalactamases:ACT	NA
contig00667	1332	1913	FOSA	0/0	100.0	92.6	MEG_2990	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA

Home-HIM_048A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00196	1963	3195	mdf(A)_1	0/0	100	97.9	Y08743	mdf(A)	NA

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00952	197	1283	acrE	0/0	93.9	98.6	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00774	1083	1745	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00577	1958	2777	bacA	0/0	99.8	98.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00599	1392	2113	baeR	0/0	99.9	97.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00599	1	1395	baeS	0/0	99.4	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00631	1127	2500	cpxA	0/0	100.0	98.4	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00145	2675	3307	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00054	3216	4388	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00054	4405	5943	emrB	0/0	100.0	98.2	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00009	4153	5208	emrK	0/0	100.0	97.5	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00054	2559	3089	emrR	0/0	100.0	98.7	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00009	2615	4153	emrY	0/0	100.0	97.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00039	2507	4150	eptA	0/0	100.0	90.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00706	208	1401	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00086	3660	4793	Escherichia_coli_ampC	0/0	100.0	98.1	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00108	2314	3471	Escherichia_coli_ampH	0/0	100.0	97.4	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00052	1080	1412	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00196	1963	3195	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00009	5732	6346	evgA	0/0	100.0	98.9	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00009	6351	9944	evgS	0/0	100.0	96.2	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00334	21	749	gadW	0/0	100.0	99.6	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00926	365	1189	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00684	1	632	kdpE	0/0	93.2	96.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00059	5216	5599	marA	0/0	100.0	98.2	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00334	1112	4225	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00353	733	1959	mdtG	0/0	100.0	98.1	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00266	367	1398	mdtN	0/0	100.0	95.5	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00266	1398	3449	mdtO	0/0	100.0	96.9	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00266	3446	4912	mdtP	0/0	100.0	97.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00051	5071	6819	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00159	4360	5328	pmrF	0/0	100.0	97.8	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00044	6944	8431	tolC	0/0	100.0	98.1	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00086	3660	4793	(Bla)AmpC2_Ecoli	0/0	100	98.1	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00108	2314	3471	(Bla)ampH_Ecoli	0/0	100	97.4	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00086	3660	4793	(Bla)AmpC2_Ecoli	0/0	100	98.1	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00108	2314	3471	(Bla)ampH_Ecoli	0/0	100	97.4	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00706	208	1401	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00952	197	1283	ACRE	0/0	93.9	98.6	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00774	1083	1745	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00108	2314	3471	AMPH	0/0	100.0	97.4	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00406	1889	3742	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00577	1958	2777	BACA	0/0	99.8	98.4	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00599	1392	2113	BAER	0/0	99.9	97.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00599	1	1395	BAES	0/0	99.4	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00005	14028	15218	BCR	0/0	100.0	96.3	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00086	3660	4793	BLAEC	0/0	100.0	99.9	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00631	432	1130	CPXAR	0/0	100.0	97.8	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00631	1127	2500	CPXAR	0/0	100.0	98.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00145	2675	3307	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00054	3216	4388	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00054	4405	5943	EMRB	0/0	100.0	98.2	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00100	2625	3815	EMRD	0/0	100.0	98.2	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00009	4153	5316	EMRK	0/0	100.0	97.3	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00054	2559	3089	EMRR	0/0	100.0	98.7	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00009	2615	4153	EMRY	0/0	100.0	97.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00039	2507	4150	EPTA	0/0	100.0	90.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00009	6351	9944	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00334	21	749	GADW	0/0	100.0	99.6	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00926	365	1189	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00684	1	632	KDPE	0/0	93.2	96.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00059	5216	5605	MARA	0/0	100.0	98.2	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00059	5620	6054	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00196	1963	3195	MDFA	0/0	100.0	98.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00334	1112	4225	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00353	733	1959	MDTG	0/0	100.0	98.2	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00084	6685	7014	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00084	6333	6698	MDTJ	0/0	100.0	97.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00501	1824	3197	MDTK	0/0	100.0	98.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00266	367	1398	MDTN	0/0	100.0	95.5	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00266	1398	3449	MDTO	0/0	100.0	96.9	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00266	3446	4912	MDTP	0/0	100.0	97.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00051	5071	6819	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00052	1080	1412	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00159	4360	5328	PMRF	0/0	100.0	97.8	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00110	5335	6204	ROBA	0/0	100.0	97.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA

Home-HIM_068B

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01906	205	781	CRP	0/0	91.2	99.3	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00049	105	1643	emrB	0/0	100.0	99.8	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig01375	1	1008	emrK	0/0	95.5	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00472	161	691	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00236	1	1568	eptA	0/0	95.4	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00401	67	1260	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00761	412	1545	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig01066	1	1276	Escherichia_coli_ampC1_beta-lactamase	0/0	97.8	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig01206	311	925	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00908	2	826	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00010	3508	3921	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00624	650	1033	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00975	1	1130	mdtA	0/0	90.5	97.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00244	918	2075	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00117	909	2117	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00072	651	2399	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01066	1	1276	(Bla)AmpC1_Ecoli	0/0	97.8	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00761	412	1545	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01066	1	1276	(Bla)AmpC1_Ecoli	0/0	97.8	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00761	412	1545	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00401	67	1260	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00761	412	1545	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig01079	293	991	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig01906	205	781	CRP	0/0	91.2	99.3	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00049	105	1643	EMRB	0/0	100.0	99.8	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00472	161	691	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00236	1	1568	EPTA	0/0	95.4	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00908	2	826	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00010	3508	3921	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00624	644	1033	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00624	195	629	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00975	1	1130	MDTA	0/0	90.5	97.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00244	918	2075	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00117	909	2117	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00877	1000	1365	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00072	651	2399	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig01066	1	1276	PBP4B	0/0	97.8	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig01024	199	1068	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00784	766	1088	SOXS	0/0	99.7	99.4	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA

Home-HIM_071A

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00220	2614	3276	acrS	0/0	100.0	99.8	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00904	49	868	bacA	0/0	99.8	98.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00675	617	1339	baeR	0/0	100.0	98.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00388	620	1252	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00173	522	1694	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00328	1774	2829	emrK	0/0	100.0	98.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00173	1821	2351	emrR	0/0	100.0	99.6	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00328	236	1774	emrY	0/0	100.0	98.6	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00071	409	2052	eptA	0/0	100.0	99.5	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00086	158	1291	Escherichia_coli_ampC	0/0	100.0	97.6	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00014	3981	5138	Escherichia_coli_ampH	0/0	100.0	98.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00863	138	752	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00776	20	748	gadW	0/0	100.0	94.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00958	584	1408	gadX	0/0	100.0	98.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00017	1186	1599	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00288	951	1334	marA	0/0	100.0	99.2	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00108	2447	3604	mdtE	0/0	100.0	99.2	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00407	517	1743	mdtG	0/0	100.0	98.7	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00179	1801	3033	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00857	364	1395	mdtN	0/0	100.0	98.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00202	60	1526	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig01697	7	483	mphB	0/0	100.0	98.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00380	470	1957	tolC	0/0	100.0	98.8	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00086	158	1291	(Bla)AmpC2_Ecoli	0/0	100	97.6	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00014	3981	5138	(Bla)ampH_Ecoli	0/0	100	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00086	158	1291	(Bla)AmpC2_Ecoli	0/0	100	97.6	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00014	3981	5138	(Bla)ampH_Ecoli	0/0	100	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00220	2614	3276	ACRS	0/0	100.0	99.8	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00014	3981	5138	AMPH	0/0	100.0	98.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00199	1569	3421	ASMA	0/0	100.0	98.9	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00904	49	868	BACA	0/0	99.8	98.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00675	617	1339	BAER	0/0	100.0	98.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00852	1	1172	BCR	0/0	98.4	97.3	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00086	158	1291	BLAEC	0/0	100.0	99.1	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00388	620	1252	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00173	522	1694	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00328	1774	2869	EMRK	0/0	94.2	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00173	1821	2351	EMRR	0/0	100.0	99.6	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00328	236	1774	EMRY	0/0	100.0	98.6	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00071	409	2052	EPTA	0/0	100.0	99.5	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00776	20	748	GADW	0/0	100.0	99.2	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00958	584	1408	GADX	0/0	100.0	98.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00017	1186	1599	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00288	945	1334	MARA	0/0	100.0	99.2	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00288	497	931	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00108	2447	3604	MDTE	0/0	100.0	99.2	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00407	517	1743	MDTG	0/0	100.0	98.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig01182	96	425	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00179	1801	3033	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00857	364	1395	MDTN	0/0	100.0	98.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00202	60	1526	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig01697	7	483	MPHB	0/0	100.0	98.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00476	297	1166	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00838	25	347	SOXS	0/0	99.7	98.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA

Home-HIM_072A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00100	2676	3149	dfrA15_2	0/0	100	100.0	AF221900	dfrA15	Trimethoprim
contig00100	439	1305	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00980	187	1344	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig01545	98	917	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00090	2806	4209	baeS	0/0	100.0	99.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig01048	1	1362	cpxA	0/0	99.1	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00102	447	1079	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00100	2676	3149	dfrA15	0/0	100.0	100.0	KF534911:39-513	dfrA15 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig01093	286	1321	emrK	0/0	98.1	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01525	31	561	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00026	4748	5905	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig01440	206	820	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00252	97	825	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01473	225	984	gadX	0/0	92.1	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00707	177	1424	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00384	573	1799	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00020	3138	4604	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00214	349	1317	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00100	439	1278	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00048	3489	4976	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00100	1783	2584	(AGly)aadA1-pm	0/0	96.5	96.4	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00026	4748	5905	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00100	439	1278	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00100	2676	3149	(Tmt)dfrA15b	0/0	100.0	99.2	AJ867237:177-650	(Tmt)dfrA15b	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00100	1783	2584	(AGly)aadA1-pm	0/0	96.5	96.4	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00026	4748	5905	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00100	439	1278	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00100	2676	3149	(Tmt)dfrA15b	0/0	100.0	99.2	AJ867237:177-650	(Tmt)dfrA15b	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00980	187	1344	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00026	4748	5905	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig01545	98	917	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00090	2806	4209	BAES	0/0	100.0	99.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00211	1263	2453	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig01048	1	1362	CPXAR	0/0	99.1	99.6	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00102	447	1079	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00100	2676	3149	DFRA	0/0	100.0	99.4	MEG_2492	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00183	2230	3353	EMRD	0/0	94.4	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig01525	31	561	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00252	97	825	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01473	225	984	GADX	0/0	92.1	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01387	346	780	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00707	177	1424	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00384	573	1799	MDTG	0/0	100.0	99.4	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00020	3138	4604	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00214	349	1317	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00986	176	1045	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00124	2083	2406	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00100	312	1279	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA

Home-HIM_073B

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00015	2698	3534	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00015	3884	4366	dfrA14_5	0/0	100	99.8	DQ388123	dfrA14	Trimethoprim
contig00015	4966	5781	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00015	2698	3534	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00981	174	896	baeR	0/0	100.0	96.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00146	2306	2938	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00015	3884	4366	dfrA14	0/0	100.0	100.0	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00422	1	1103	emrA	0/0	94.0	97.8	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig02586	1	523	emrR	0/0	98.5	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00131	1	1481	eptA	0/0	90.1	97.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00039	2681	3814	Escherichia_coli_ampC	0/0	100.0	97.9	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig01343	129	461	Escherichia_coli_emrE	0/0	100.0	91.6	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01046	20	634	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig01060	168	896	gadW	0/0	100.0	96.6	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01564	1	824	gadX	0/0	99.9	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig02681	168	560	H-NS	0/0	94.9	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00334	561	1718	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00069	147	2198	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00069	2195	3661	mdtP	0/0	100.0	96.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00976	728	1202	mphB	0/0	99.6	97.0	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00015	4966	5781	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00757	1	1535	yojI	0/0	93.4	97.5	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00015	2698	3534	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00039	2681	3814	(Bla)AmpC2_Ecoli	0/0	100	97.9	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00015	4966	5781	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00015	3884	4357	(Tmt)dfrA14	0/0	100	99.8	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00015	2698	3534	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00039	2681	3814	(Bla)AmpC2_Ecoli	0/0	100	97.9	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00015	4966	5781	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00015	3884	4357	(Tmt)dfrA14	0/0	100	99.8	GU726917:72-545	(Tmt)dfrA14	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00015	2698	3534	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00981	174	896	BAER	0/0	100.0	96.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00907	158	1348	BCR	0/0	100.0	96.4	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00039	2681	3814	BLAEC	0/0	100.0	99.2	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig01691	177	875	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00146	2306	2938	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00015	3884	4357	DFRA	0/0	100.0	100.0	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00422	1	1103	EMRA	0/0	94.0	97.8	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig02586	1	523	EMRR	0/0	98.5	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00131	1	1481	EPTA	0/0	90.1	97.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01060	168	896	GADW	0/0	100.0	96.8	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01564	1	824	GADX	0/0	99.9	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig02681	168	560	HNS	0/0	94.9	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00334	561	1718	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00251	1083	1412	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00251	731	1096	MDTJ	0/0	100.0	97.8	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00069	147	2198	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00069	2195	3661	MDTP	0/0	100.0	96.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00976	728	1202	MPHB	0/0	99.6	97.0	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig01343	129	461	MVRC	0/0	100.0	91.6	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00733	548	1417	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig01022	129	451	SOXS	0/0	99.7	97.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00015	4966	5781	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00757	1	1535	YOGI	0/0	93.4	97.5	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Home-HIM_075A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00029	15382	16185	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00029	14546	15382	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00029	12826	13299	dfrA1_10	0/0	100.0	99.8	AF203818	dfrA1	Trimethoprim
contig00307	4536	4958	fosA7_1	0/0	100.0	94.1	LAPJ01000014	fosA7	Fosfomycin
contig00019	7740	8972	mdf(A)_1	0/0	100.0	98.5	Y08743	mdf(A)
contig00029	10598	11464	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00029	16246	17061	sul2_3	0/0	100.0	100.0	HQ840942	sul2	Sulfamethoxazole
contig00113	1749	2995	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00228	3904	7053	acrB	0/0	100.0	99.2	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00158	5904	9017	acrD	0/0	100.0	99.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00175	5122	8226	acrF	0/0	100.0	98.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00537	392	1054	acrS	0/0	100.0	98.8	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00029	15382	16185	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00029	14546	15382	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00068	93	912	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00191	4487	5209	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00191	3087	4490	baeS	0/0	100.0	99.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00483	1368	2741	cpxA	0/0	100.0	98.7	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00297	2156	2788	CRP	0/0	100.0	99.5	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00029	12826	13299	dfrA1	0/0	100.0	100.0	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00363	1	1150	emrA	0/0	98.0	98.5	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00319	1	1531	emrB	0/0	99.5	99.8	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00093	1345	2400	emrK	0/0	100.0	99.6	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00363	1277	1807	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00131	2495	4138	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00228	2688	3881	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00037	3213	4346	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	21474	22778	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00119	4910	6067	Escherichia_coli_ampH	0/0	100.0	98.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00073	1397	1729	Escherichia_coli_emrE	0/0	100.0	98.8	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00019	7740	8972	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00093	2924	3538	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00093	3543	7136	evgS	0/0	100.0	98.9	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00307	4536	4958	FosA7	0/0	100.0	94.1	LAPJ01000014.1:36822-37245	fosA7 is an enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.	fosfomycin
contig00094	1568	2296	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00094	376	1200	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00282	5387	5800	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00674	347	996	kdpE	0/0	95.9	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00219	5514	5897	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00288	4317	5564	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00288	1195	4317	mdtB	0/0	100.0	97.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00094	5797	6954	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00094	2659	5772	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00372	2316	3542	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00066	9270	10478	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00070	1436	2668	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00192	6643	7674	mdtN	0/0	100.0	98.1	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00192	4592	6643	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00192	3129	4595	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00033	4431	4905	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00008	15972	17720	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00116	9184	10152	pmrF	0/0	100.0	99.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00029	10598	11437	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00029	16246	17061	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00113	1749	2995	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00078	5917	7404	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00324	1393	3036	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00029	11942	12743	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00029	15382	16185	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00029	14546	15382	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00006	21474	22778	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00037	3213	4346	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00119	4910	6067	(Bla)ampH_Ecoli	0/0	100.0	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00105	1015	2916	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00307	4536	4958	(Fcyn)FosA7	0/0	100.0	94.1	LAPJ01000014:36823-37245	(Fcyn)FosA7	NA
contig00029	10598	11437	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00029	16246	17061	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00113	1749	3023	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00113	1068	1718	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00029	12826	13299	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00029	11942	12743	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00029	15382	16185	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00029	14546	15382	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00006	21474	22778	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00037	3213	4346	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00119	4910	6067	(Bla)ampH_Ecoli	0/0	100.0	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00105	1015	2916	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00307	4536	4958	(Fcyn)FosA7	0/0	100.0	94.1	LAPJ01000014:36823-37245	(Fcyn)FosA7	NA
contig00029	10598	11437	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00029	16246	17061	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00113	1749	3023	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00113	1068	1718	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00029	12826	13299	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00228	2688	3881	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00228	3904	7053	ACRB	0/0	100.0	99.2	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00158	5904	9017	ACRD	0/0	100.0	99.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00175	5122	8226	ACRF	0/0	100.0	98.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00537	392	1054	ACRS	0/0	100.0	98.8	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00119	4910	6067	AMPH	0/0	100.0	98.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00029	11942	12743	ANT3-DPRIME	0/0	96.5	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00029	15382	16209	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00029	14546	15382	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00164	7396	9248	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00068	93	912	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00191	4487	5209	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00191	3087	4490	BAES	0/0	100.0	99.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00275	1757	2947	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00037	3213	4346	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00483	673	1371	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00483	1368	2741	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00297	2156	2788	CRP	0/0	100.0	99.5	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00029	12826	13299	DFRA	0/0	100.0	99.8	MEG_2528	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00363	1	1150	EMRA	0/0	98.0	98.5	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00319	1	1531	EMRB	0/0	99.5	99.8	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00017	22477	23667	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00093	1345	2508	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00363	1277	1807	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00131	2495	4138	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00093	3543	7136	EVGS	0/0	100.0	98.9	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00307	4536	4958	FOSA	0/0	100.0	94.1	MEG_2988	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00094	1568	2296	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00094	376	1200	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00282	5387	5800	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00674	347	996	KDPE	0/0	95.9	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00219	5514	5903	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00219	5917	6351	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00019	7740	8972	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00288	4317	5564	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00288	1195	4317	MDTB	0/0	100.0	97.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00094	5797	6954	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00094	2659	5772	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00372	2316	3542	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00066	9270	10478	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00420	3167	3486	MDTI	0/0	97.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00122	9933	11174	MDTK	0/0	90.4	99.2	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00070	1436	2668	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00192	6643	7674	MDTN	0/0	100.0	98.1	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00192	4592	6643	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00192	3129	4595	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00033	4431	4905	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00008	15972	17720	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00073	1397	1729	MVRC	0/0	100.0	98.8	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00105	1015	2916	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00006	21474	22778	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00116	9184	10152	PMRF	0/0	100.0	99.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00060	11897	12766	ROBA	0/0	100.0	99.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00411	1934	2257	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00029	10471	11438	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00029	16246	17061	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00113	1749	3023	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00324	1393	3036	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Home-HIM_82A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00024	7677	8480	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00024	6841	7677	aph(6)-Id_1	0/0	100	99.9	M28829	aph(6)-Id	Streptomycin
contig00935	575	1435	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig01210	42	551	dfrA8_1	0/0	100	100.0	U10186	dfrA8	Trimethoprim
contig00024	1383	2304	mph(A)_2	1/1	100	99.6	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00024	8541	9356	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	2457	5606	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00024	7677	8480	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00024	6841	7677	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00039	5548	6270	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00039	4148	5551	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00643	1037	2410	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00305	566	1198	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01210	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00412	2249	3308	emrA	0/0	90.4	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00412	694	2232	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00705	386	1441	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00276	1167	2810	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	1241	2434	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00277	2915	4048	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00131	4387	5691	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00363	1586	2314	gadW	0/0	100.0	94.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00363	394	1218	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00040	3528	3941	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00461	1226	2383	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00570	731	1957	mdtG	0/0	100.0	99.7	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00168	1239	2447	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00798	481	1713	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00054	6565	7596	mdtN	0/0	100.0	99.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00054	3129	4595	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00024	1383	2288	mphA	0/0	100.0	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00230	1699	2175	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	3126	4874	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00024	8541	9356	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00935	575	1435	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00021	5667	7154	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00617	934	2517	yojI	0/0	96.3	99.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00024	7677	8480	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00024	6841	7677	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00131	4387	5691	(Bla)AmpC1_Ecoli	0/0	100	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00277	2915	4048	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00935	575	1435	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00024	1383	2288	(MLS)mph(A)	0/0	100	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00024	8541	9356	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig01210	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00024	7677	8480	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00024	6841	7677	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00131	4387	5691	(Bla)AmpC1_Ecoli	0/0	100	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00277	2915	4048	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00935	575	1435	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00024	1383	2288	(MLS)mph(A)	0/0	100	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00024	8541	9356	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig01210	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	1241	2434	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	2457	5606	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00277	2915	4048	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00024	7677	8504	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00024	6841	7677	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00039	5548	6270	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00039	4148	5551	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00643	342	1040	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00643	1037	2410	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00305	566	1198	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01210	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00412	2249	3308	EMRA	0/0	90.4	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00412	694	2232	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00013	164	1354	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00705	386	1549	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00276	1167	2810	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00363	1586	2314	GADW	0/0	100.0	99.9	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00363	394	1218	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00040	3528	3941	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00400	2837	3271	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00461	1226	2383	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00570	731	1957	MDTG	0/0	100.0	99.7	MEG_3754	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00168	1239	2447	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00901	380	709	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00901	28	393	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00798	481	1713	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00054	6565	7596	MDTN	0/0	100.0	99.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00054	3129	4595	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00024	1383	2304	MPHA	1/1	100.0	99.6	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00230	1699	2175	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	3126	4874	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00131	4387	5691	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00840	1554	1870	SOXS	0/0	97.8	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00024	8541	9356	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00617	934	2517	YOGI	0/0	96.3	99.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Home-KAT_009A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00753	119	922	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig01741	1	839	blaTEM-1B_1	0/0	97.4	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00681	764	1337	dfrA7_5	3/4	100.0	98.8	AJ419170	dfrA7	Trimethoprim
contig00295	558	1790	mdf(A)_1	0/0	100.0	97.6	Y08743	mdf(A)
contig00753	983	1798	sul2_3	0/0	100.0	100.0	HQ840942	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01035	197	1354	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00753	119	922	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00021	41	860	bacA	0/0	99.8	97.6	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig01020	843	1564	baeR	0/0	99.9	97.8	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00545	1117	2490	cpxA	0/0	100.0	97.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig01089	878	1475	CRP	0/0	94.5	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00681	864	1337	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00627	136	1674	emrB	0/0	100.0	98.2	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00788	899	1954	emrK	0/0	100.0	97.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01310	71	601	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00112	1141	2784	eptA	0/0	100.0	98.1	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig01099	64	1257	Escherichia_coli_acrA	0/0	100.0	99.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00033	3096	4229	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00295	558	1790	Escherichia_coli_mdfA	0/0	100.0	96.0	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00773	344	958	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00716	1	701	gadW	0/0	96.2	95.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01401	192	1016	gadX	0/0	100.0	96.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00109	1021	1404	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00277	154	1401	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00331	1	3040	mdtC	0/0	98.8	96.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig01054	403	1535	mdtE	0/0	97.8	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00494	718	1944	mdtG	0/0	100.0	98.0	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00378	427	2175	msbA	0/0	100.0	98.8	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00402	754	1722	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00753	983	1798	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig01741	1	839	TEM-1	0/0	97.4	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00251	1617	3104	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00824	78	1244	ugd	0/0	100.0	99.8	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00753	119	922	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00033	3096	4229	(Bla)AmpC2_Ecoli	0/0	100.0	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig01741	1	839	(Bla)blaTEM-105	0/0	97.4	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00753	983	1798	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig01082	454	1104	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00681	864	1337	(Tmt)dhfr7	0/0	100.0	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00753	119	922	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00033	3096	4229	(Bla)AmpC2_Ecoli	0/0	100.0	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig01741	1	839	(Bla)blaTEM-105	0/0	97.4	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00753	983	1798	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig01082	454	1104	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00681	864	1337	(Tmt)dhfr7	0/0	100.0	100.0	X58425:594-1067	(Tmt)dhfr7	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01099	64	1257	ACRA	0/0	100.0	99.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig01035	197	1354	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00753	119	946	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00021	41	860	BACA	0/0	99.8	97.6	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig01020	843	1564	BAER	0/0	99.9	97.8	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00033	3096	4229	BLAEC	0/0	100.0	98.2	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00545	422	1120	CPXAR	0/0	100.0	99.6	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00545	1117	2490	CPXAR	0/0	100.0	98.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig01089	878	1475	CRP	0/0	94.5	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00681	864	1337	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00627	136	1674	EMRB	0/0	100.0	98.2	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00788	899	1984	EMRK	0/0	93.3	97.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01310	71	601	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00112	1141	2784	EPTA	0/0	100.0	98.1	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00716	1	701	GADW	0/0	96.2	97.4	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01401	192	1016	GADX	0/0	100.0	96.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00109	1015	1404	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00109	567	1001	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00295	558	1790	MDFA	0/0	100.0	97.7	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00277	154	1401	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00331	1	3040	MDTC	0/0	98.8	96.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig01054	403	1535	MDTE	0/0	97.8	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00494	718	1944	MDTG	0/0	100.0	98.2	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00380	2576	2905	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00206	1709	3081	MDTK	0/0	99.9	98.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00378	427	2175	MSBA	0/0	100.0	98.8	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00402	754	1722	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00741	1207	2076	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00753	983	1798	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00824	78	1244	UGD	0/0	100.0	99.8	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

Home-KAT_013A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	3746	4549	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00010	2910	3746	aph(6)-Id_1	0/0	100	99.9	M28829	aph(6)-Id	Streptomycin
contig00291	575	1435	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig01148	43	552	dfrA8_1	0/0	100	100.0	U10186	dfrA8	Trimethoprim
contig00010	4610	5425	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00489	742	1947	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00282	1233	2390	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	3746	4549	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00010	2910	3746	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig01472	115	936	bacA	0/0	100.0	99.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00392	909	1631	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00060	2600	3973	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00030	916	1548	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01148	43	552	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00673	515	1570	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01023	218	1298	Escherichia_coli_acrA	0/0	90.5	99.9	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	6574	7707	Escherichia_coli_ampC	0/0	100.0	98.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00473	617	949	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00314	1	1212	mdtA	0/0	97.1	99.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00503	89	1246	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00131	1287	2513	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00200	532	1764	mdtM	0/0	100.0	97.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00010	4610	5425	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00291	575	1435	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00489	742	1947	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00888	1	1443	tolC	0/0	97.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	3746	4549	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00010	2910	3746	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00003	6574	7707	(Bla)AmpC2_Ecoli	0/0	100	98.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00291	575	1435	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00063	839	2740	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00010	4610	5425	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00489	742	1947	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig01148	43	552	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	3746	4549	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00010	2910	3746	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00003	6574	7707	(Bla)AmpC2_Ecoli	0/0	100	98.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00291	575	1435	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00063	839	2740	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00010	4610	5425	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00489	742	1947	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig01148	43	552	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01023	218	1298	ACRA	0/0	90.5	99.9	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00282	1233	2390	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00010	3746	4573	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00010	2910	3746	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig01472	115	936	BACA	0/0	100.0	99.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00392	909	1631	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00003	6574	7707	BLAEC	0/0	100.0	99.7	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00060	1905	2603	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00060	2600	3973	CPXAR	0/0	100.0	99.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00030	916	1548	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01148	43	552	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig01048	1	1093	EMRD	0/0	91.8	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00673	515	1655	EMRK	0/0	98.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00314	1	1212	MDTA	0/0	97.1	99.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00503	89	1246	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00131	1287	2513	MDTG	0/0	100.0	99.8	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig02237	200	529	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00200	532	1764	MDTM	0/0	100.0	97.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00473	617	949	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00063	839	2740	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00048	3214	4083	ROBA	0/0	100.0	100.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00010	4610	5425	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00489	742	1947	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA

Home-KAT_023A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01332	257	1117	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig01365	467	1040	dfrA7_5	3/4	100	98.8	AJ419170	dfrA7	Trimethoprim
contig00837	778	1593	sul2_3	0/0	100	100.0	HQ840942	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01835	1	773	bacA	0/0	94.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00394	1117	2490	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00092	445	1077	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01365	567	1040	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00069	2755	3927	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00069	1200	2738	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00990	342	1397	emrK	0/0	100.0	100.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00069	4054	4584	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00098	2245	3888	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00359	535	1728	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00025	3715	4848	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00684	399	1556	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig01558	25	639	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00270	1	718	gadW	0/0	98.5	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01283	371	1195	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00074	4084	4497	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00108	2588	2971	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig01407	1	1104	mdtE	0/0	95.3	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00229	1145	2371	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00065	919	2385	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00222	1329	1805	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00837	778	1593	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig01332	257	1117	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00025	3715	4848	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00684	399	1556	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01332	257	1117	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00837	778	1593	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig01365	567	1040	(Tmt)dhfr7	0/0	100	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00025	3715	4848	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00684	399	1556	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01332	257	1117	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00837	778	1593	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig01365	567	1040	(Tmt)dhfr7	0/0	100	100.0	X58425:594-1067	(Tmt)dhfr7	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00359	535	1728	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00025	3715	4848	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00684	399	1556	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig01835	1	773	BACA	0/0	94.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00394	422	1120	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00394	1117	2490	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00092	445	1077	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01365	567	1040	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00069	2755	3927	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00069	1200	2738	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00990	342	1471	EMRK	0/0	97.1	100.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00069	4054	4584	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00098	2245	3888	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00270	1	718	GADW	0/0	98.5	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01283	371	1195	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00074	4084	4497	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00108	2582	2971	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00108	2134	2568	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig01407	1	1104	MDTE	0/0	95.3	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00229	1145	2371	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00861	1	324	MDTI	0/0	98.2	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00561	251	1624	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00065	919	2385	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00222	1329	1805	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00289	1516	1839	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00837	778	1593	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Home-KAT_039B

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01083	173	655	dfrA14_5	0/0	100	99.6	DQ388123	dfrA14	Trimethoprim
contig00834	192	1007	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00026	2130	2792	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00657	400	1173	bacA	0/0	94.2	99.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig01083	173	655	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00546	278	1275	emrK	0/0	94.5	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00024	517	2160	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00207	7	1755	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00683	159	1127	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00834	192	1007	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00834	192	1007	(Sul)sul2	0/0	100	100	EU360945:1617-2432	(Sul)sul2	NA
contig01083	173	646	(Tmt)dfrA14	0/0	100	100	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00834	192	1007	(Sul)sul2	0/0	100	100	EU360945:1617-2432	(Sul)sul2	NA
contig01083	173	646	(Tmt)dfrA14	0/0	100	100	GU726917:72-545	(Tmt)dfrA14	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00026	2130	2792	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00657	400	1173	BACA	0/0	94.2	99.0	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig01083	173	646	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00024	517	2160	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01274	422	855	MARR	0/0	99.8	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig02042	245	610	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00129	1	1242	MDTK	0/0	90.4	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00207	7	1755	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00683	159	1127	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00834	192	1007	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Hosp-BWE_048

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	1975	2811	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00007	3161	3643	dfrA14_5	0/0	100	99.8	DQ388123	dfrA14	Trimethoprim
contig00007	4243	5058	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	1975	2811	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00559	529	1161	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00007	3161	3643	dfrA14	0/0	100.0	100.0	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00454	523	1578	emrK	0/0	100.0	100.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00711	197	1355	Escherichia_coli_acrA	0/0	97.1	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig01008	192	1016	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00232	495	908	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00031	1857	3014	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00004	3545	5293	msbA	0/0	100.0	98.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00007	4243	5058	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00002	4507	5994	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	1975	2811	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00007	4243	5058	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00007	3161	3634	(Tmt)dfrA14	0/0	100	99.8	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	1975	2811	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00007	4243	5058	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00007	3161	3634	(Tmt)dfrA14	0/0	100	99.8	GU726917:72-545	(Tmt)dfrA14	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00711	197	1355	ACRA	0/0	97.1	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00007	1975	2811	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00559	529	1161	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00007	3161	3634	DFRA	0/0	100.0	100.0	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00454	523	1652	EMRK	0/0	97.1	100.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01008	192	1016	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00232	495	908	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00031	1857	3014	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig02252	317	624	MDTI	0/0	93.3	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig02252	1	330	MDTJ	0/0	90.2	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	3545	5293	MSBA	0/0	100.0	98.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00007	4243	5058	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Hosp-BWE_054

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1697	2485	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00354	843	1646	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00354	7	843	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00971	109	969	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00268	2616	3089	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00356	2699	3931	mdf(A)_1	0/0	100	97.8	Y08743	mdf(A)
contig00268	311	1177	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00354	1707	2522	sul2_3	0/0	100	100.0	HQ840942	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1697	2485	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00994	197	1354	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig01328	136	758	acrS	0/0	94.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00354	843	1646	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00354	7	843	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00050	8075	8894	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00024	2920	3641	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00024	1520	2923	baeS	0/0	100.0	90.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00715	931	2304	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00248	1517	2149	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00268	2616	3089	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00375	2087	3625	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00052	1466	2521	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00765	435	965	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00052	1	1466	emrY	0/0	95.3	97.5	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00315	2466	4109	eptA	0/0	100.0	91.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00094	6235	7428	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	1262	2395	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00190	4295	5452	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00356	2699	3931	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00052	3045	3659	evgA	0/0	100.0	98.9	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00052	3664	7257	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00596	1558	2286	gadW	0/0	100.0	99.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00596	365	1189	gadX	0/0	100.0	93.7	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00593	2426	2839	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00022	1539	1922	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00829	177	1424	mdtA	0/0	100.0	95.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00251	2925	4082	mdtE	0/0	100.0	98.3	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00251	1	2900	mdtF	0/0	93.1	97.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00623	743	1969	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00032	9316	10524	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00341	1	1194	mdtM	0/0	96.8	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00123	395	1426	mdtN	0/0	100.0	96.3	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00123	1426	3477	mdtO	0/0	100.0	97.2	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00123	3474	4940	mdtP	0/0	100.0	98.1	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00342	2197	3165	pmrF	0/0	100.0	97.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00268	311	1150	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00354	1707	2522	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00971	109	969	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00069	6913	8400	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig01114	62	1183	ugd	0/0	96.1	99.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00116	6212	7855	yojI	0/0	100.0	97.3	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1697	2485	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00354	843	1646	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00354	7	843	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00011	1262	2395	(Bla)AmpC2_Ecoli	0/0	100	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00190	4295	5452	(Bla)ampH_Ecoli	0/0	100	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00971	109	969	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00150	4681	6582	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00268	311	1150	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00354	1707	2522	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00268	2616	3089	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1697	2485	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00354	843	1646	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00354	7	843	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00011	1262	2395	(Bla)AmpC2_Ecoli	0/0	100	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00190	4295	5452	(Bla)ampH_Ecoli	0/0	100	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00971	109	969	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00150	4681	6582	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00268	311	1150	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00354	1707	2522	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00268	2616	3089	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	6235	7428	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00994	197	1354	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig01328	136	758	ACRS	0/0	94.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00190	4295	5452	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00268	1697	2485	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00354	843	1670	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00354	7	843	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00402	1830	3682	ASMA	0/0	100.0	97.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00050	8075	8894	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00024	2920	3641	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00024	1520	2923	BAES	0/0	100.0	90.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00688	1	1184	BCR	0/0	99.4	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00011	1262	2395	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00715	236	934	CPXAR	0/0	100.0	97.8	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00715	931	2304	CPXAR	0/0	100.0	98.9	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00248	1517	2149	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00268	2616	3089	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00375	2087	3625	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00482	2419	3495	EMRD	0/0	90.4	97.4	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00052	1466	2629	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00765	435	965	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00052	1	1466	EMRY	0/0	95.3	97.6	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00315	2466	4109	EPTA	0/0	100.0	91.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00052	3664	7257	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00596	1558	2286	GADW	0/0	100.0	99.9	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00596	365	1189	GADX	0/0	100.0	93.7	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00593	2426	2839	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00022	1539	1928	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00022	1943	2377	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00356	2699	3931	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00829	177	1424	MDTA	0/0	100.0	95.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00251	2925	4082	MDTE	0/0	100.0	98.3	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00251	1	2900	MDTF	0/0	93.1	97.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00623	743	1969	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00032	9316	10524	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00771	683	1012	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00771	331	696	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00330	1615	2987	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00341	1	1194	MDTM	0/0	96.8	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00123	395	1426	MDTN	0/0	100.0	96.3	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00123	1426	3477	MDTO	0/0	100.0	97.2	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00123	3474	4940	MDTP	0/0	100.0	98.1	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00150	4681	6582	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00342	2197	3165	PMRF	0/0	100.0	97.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00101	1538	2407	ROBA	0/0	100.0	99.7	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00412	1049	1371	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00268	184	1151	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00354	1707	2522	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00971	91	1336	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig01114	62	1183	UGD	0/0	96.1	99.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00116	6212	7855	YOGI	0/0	100.0	97.3	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Hosp-BWE_076

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00014	2919	3755	aph(6)-Id_1	0/0	100	99.9	M28829	aph(6)-Id	Streptomycin
contig00800	344	1204	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00931	42	551	dfrA8_1	0/0	100	100.0	U10186	dfrA8	Trimethoprim
contig00293	360	1175	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00014	2919	3755	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00233	15	836	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00058	620	1252	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00931	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00166	544	2082	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig01094	376	906	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00108	105	1748	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00104	986	1600	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig01233	230	972	gadX	0/0	90.1	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00135	1623	2006	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00010	2447	3604	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00287	1329	1805	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00301	323	1291	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00293	360	1175	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00800	344	1204	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00014	2919	3755	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00800	344	1204	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00293	360	1175	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00931	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00014	2919	3755	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00800	344	1204	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00293	360	1175	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00931	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00014	2919	3755	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00233	15	836	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00058	620	1252	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00931	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00166	544	2082	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig01094	376	906	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00108	105	1748	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01233	230	972	GADX	0/0	90.1	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00135	1617	2006	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00135	1169	1603	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00010	2447	3604	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00287	1329	1805	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00301	323	1291	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00293	360	1175	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Hosp-BWE_106

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00170	804	1606	aph(3’’)-Ib_2	0/0	99.9	100.0	AF024602	aph(3’’)-Ib	Streptomycin
contig00170	1	804	aph(6)-Id_1	0/0	96.1	100.0	M28829	aph(6)-Id	Streptomycin
contig01367	1	819	blaTEM-1C_1	0/0	95.1	100.0	FJ560503	blaTEM-1C	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00361	805	1278	dfrA1_10	0/0	100.0	99.8	AF203818	dfrA1	Trimethoprim

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00170	804	1607	APH(3’’)-Ib	0/0	100.0	99.9	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00170	1	804	APH(6)-Id	0/0	96.1	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00361	805	1278	dfrA1	0/0	100.0	100.0	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00061	1010	2526	emrB	0/0	98.6	98.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00537	291	1284	emrK	0/0	94.1	97.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00006	1	1613	eptA	0/0	98.1	98.1	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig02880	68	467	H-NS	0/0	96.6	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00410	357	831	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig01367	1	819	TEM-1	0/0	95.1	100.0	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00170	804	1607	(AGly)strA	0/0	100.0	100.0	AB366441:22458-23261	(AGly)strA	NA
contig00170	1	804	(AGly)strB	0/0	96.1	100.0	FJ474091:264-1100	(AGly)strB	NA
contig01367	1	819	(Bla)blaTEM-135	0/0	95.1	99.9	JQ060998:1-861	(Bla)blaTEM-135	NA
contig00361	805	1278	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00170	804	1607	(AGly)strA	0/0	100.0	100.0	AB366441:22458-23261	(AGly)strA	NA
contig00170	1	804	(AGly)strB	0/0	96.1	100.0	FJ474091:264-1100	(AGly)strB	NA
contig01367	1	819	(Bla)blaTEM-135	0/0	95.1	99.9	JQ060998:1-861	(Bla)blaTEM-135	NA
contig00361	805	1278	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00170	804	1631	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00170	1	804	APH6	0/0	96.1	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig01091	176	874	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00361	805	1278	DFRA	0/0	100.0	99.8	MEG_2528	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00061	1010	2526	EMRB	0/0	98.6	98.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00006	1	1613	EPTA	0/0	98.1	98.1	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig02880	68	467	HNS	0/0	96.6	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig01411	60	494	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00410	357	831	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00416	730	1052	SOXS	0/0	99.7	97.5	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig01367	1	819	TEM	0/0	95.1	100.0	MEG_6740	Drugs:betalactams:Class_A_betalactamases:TEM	NA

Hosp-HIM_031

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00913	364	1166	aph(3’’)-Ib_2	0/0	99.9	100	AF024602	aph(3’’)-Ib	Streptomycin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00136	1	2909	acrB	0/0	92.3	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00913	364	1167	APH(3’’)-Ib	0/0	100.0	99.9	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig01222	252	884	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00870	292	1347	emrK	0/0	100.0	98.3	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01441	189	719	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00042	2402	3939	eptA	0/0	93.5	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00047	2491	3684	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	2332	3489	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00276	420	1034	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig01599	17	841	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig02908	16	429	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00073	561	1718	mdtE	0/0	100.0	99.6	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00396	89	2003	mdtO	0/0	93.3	98.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00286	1118	1594	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00913	364	1167	(AGly)strA	0/0	100	100.0	AB366441:22458-23261	(AGly)strA	NA
contig00002	2332	3489	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00913	364	1167	(AGly)strA	0/0	100	100.0	AB366441:22458-23261	(AGly)strA	NA
contig00002	2332	3489	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00047	2491	3684	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00136	1	2909	ACRB	0/0	92.3	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	2332	3489	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00913	364	1191	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00520	873	1571	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig01222	252	884	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00993	1	1097	EMRD	0/0	92.1	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00870	292	1377	EMRK	0/0	93.3	98.3	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01441	189	719	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00042	2402	3939	EPTA	0/0	93.5	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01599	17	841	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig02908	16	429	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00073	561	1718	MDTE	0/0	100.0	99.6	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00928	435	764	MDTI	0/0	100.0	99.1	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00928	751	1116	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00396	89	2003	MDTO	0/0	93.3	98.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00286	1118	1594	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00262	422	1291	ROBA	0/0	100.0	99.4	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00141	1735	2058	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA

Hosp-HIM_045

Resfinder

## [1] "No antibiotic resitance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00964	197	1354	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00396	2471	3133	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00079	2838	3560	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00079	1438	2841	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00625	987	2360	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00722	1032	1664	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00076	3936	5108	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00076	2381	3919	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00541	1231	2286	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00076	5235	5765	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00109	1794	3437	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00611	335	1528	Escherichia_coli_acrA	0/0	100.0	99.9	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	7904	9037	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00036	2502	3659	Escherichia_coli_ampH	0/0	100.0	98.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00186	21	635	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00186	640	4233	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00243	1181	1909	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00243	1	813	gadX	0/0	98.5	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00241	1494	1907	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00496	1997	2380	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00490	1305	2462	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00218	1521	2729	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00709	414	1646	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00411	395	1426	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00437	90	1556	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00484	485	2233	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00230	1130	2296	ugd	0/0	100.0	96.7	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00477	1176	2819	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	7904	9037	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00036	2502	3659	(Bla)ampH_Ecoli	0/0	100	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00358	1082	2983	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	7904	9037	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00036	2502	3659	(Bla)ampH_Ecoli	0/0	100	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00358	1082	2983	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00611	335	1528	ACRA	0/0	100.0	99.9	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00964	197	1354	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00396	2471	3133	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00036	2502	3659	AMPH	0/0	100.0	98.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00079	2838	3560	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00079	1438	2841	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00734	817	2007	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00003	7904	9037	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00625	292	990	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00625	987	2360	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00722	1032	1664	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00076	3936	5108	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00076	2381	3919	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00465	1534	2724	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00541	1231	2394	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00076	5235	5765	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00109	1794	3437	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00186	640	4233	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00243	1181	1909	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00243	1	813	GADX	0/0	98.5	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00241	1494	1907	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00496	1991	2380	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00496	1543	1977	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00490	1305	2462	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00218	1521	2729	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00687	1415	1744	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00687	1063	1428	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00568	1275	2581	MDTK	0/0	95.1	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00709	414	1646	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00411	395	1426	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00437	90	1556	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00484	485	2233	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00358	1082	2983	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00161	3743	4612	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00394	2898	3220	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00230	1130	2296	UGD	0/0	100.0	96.7	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00477	1176	2819	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Hosp-HIM_048

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	5855	6328	dfrA1_10	0/0	100	99.8	AF203818	dfrA1	Trimethoprim
contig00005	3627	4493	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01894	36	814	bacA	0/0	94.8	98.6	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00722	578	1210	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00005	5855	6328	dfrA1	0/0	100.0	100.0	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00032	1997	3052	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01432	50	580	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00032	459	1997	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00323	1140	2333	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	4248	5381	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00024	430	1587	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00032	3576	4190	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00271	1282	2010	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00271	90	914	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01122	299	682	marA	0/0	100.0	99.2	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00075	1226	2383	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00563	191	1423	mdtM	0/0	100.0	96.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00212	1333	1809	mphB	0/0	100.0	97.9	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00154	47	1795	msbA	0/0	100.0	99.3	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00005	3627	4466	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	4971	5772	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00010	4248	5381	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00024	430	1587	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00199	931	2832	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00005	3627	4466	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig01684	45	695	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00005	5855	6328	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	4971	5772	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00010	4248	5381	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00024	430	1587	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00199	931	2832	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00005	3627	4466	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig01684	45	695	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00005	5855	6328	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00323	1140	2333	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00024	430	1587	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00005	4971	5772	ANT3-DPRIME	0/0	96.5	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig01894	36	814	BACA	0/0	94.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00010	4248	5381	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00564	869	1567	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00722	578	1210	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00005	5855	6328	DFRA	0/0	100.0	99.8	MEG_2528	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00032	1997	3160	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01432	50	580	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00032	459	1997	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00271	1282	2010	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00271	90	914	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01122	293	682	MARA	0/0	100.0	99.2	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00075	1226	2383	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00170	1611	2984	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00563	191	1423	MDTM	0/0	100.0	96.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00212	1333	1809	MPHB	0/0	100.0	97.9	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00154	47	1795	MSBA	0/0	100.0	99.3	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00199	931	2832	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00071	2328	3197	ROBA	0/0	100.0	99.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00168	761	1084	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00005	3500	4467	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA

Hosp-HIM_068

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00047	13624	14856	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)	NA

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00011	17630	20779	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00288	1	2814	acrD	0/0	90.4	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00033	8238	9395	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00033	5122	8226	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00033	9794	10456	acrS	0/0	100.0	98.8	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00723	93	912	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00058	2306	3028	baeR	0/0	100.0	98.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00058	906	2309	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00327	3587	4960	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00260	2156	2788	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00427	478	1650	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00008	8335	9390	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00427	1777	2307	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00008	6797	8335	emrY	0/0	100.0	98.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00112	2402	4045	eptA	0/0	100.0	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00011	20802	21995	Escherichia_coli_acrA	0/0	100.0	99.6	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00040	3213	4346	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00241	3891	5195	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00107	5238	6395	Escherichia_coli_ampH	0/0	100.0	99.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00047	13624	14856	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00008	9914	10528	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	10533	14126	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00365	1568	2296	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00365	376	1200	gadX	0/0	100.0	97.7	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00448	25	438	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00367	3827	4483	kdpE	0/0	96.9	97.3	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00082	1627	2010	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00295	4093	5340	mdtA	0/0	100.0	98.1	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00295	971	4093	mdtB	0/0	100.0	98.4	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00458	1236	2393	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00164	6425	7651	mdtG	0/0	100.0	98.9	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00083	9270	10478	mdtH	0/0	100.0	98.5	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00390	2061	3293	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00360	3536	4567	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00301	1	1984	mdtO	0/0	96.7	98.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00301	1981	3447	mdtP	0/0	100.0	98.3	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00037	4591	5065	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00034	4736	6484	msbA	0/0	100.0	99.3	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00174	3501	4469	pmrF	0/0	100.0	99.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00122	3476	4963	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00309	231	1397	ugd	0/0	100.0	95.5	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00446	1273	2916	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00241	3891	5195	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00040	3213	4346	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00107	5238	6395	(Bla)ampH_Ecoli	0/0	100	99.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00027	10413	12314	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00241	3891	5195	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00040	3213	4346	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00107	5238	6395	(Bla)ampH_Ecoli	0/0	100	99.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00027	10413	12314	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00011	20802	21995	ACRA	0/0	100.0	99.6	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00011	17630	20779	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00288	1	2814	ACRD	0/0	90.4	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00033	8238	9395	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00033	5122	8226	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00033	9794	10456	ACRS	0/0	100.0	98.8	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00107	5238	6395	AMPH	0/0	100.0	99.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00158	5471	7323	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00723	93	912	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00058	2306	3028	BAER	0/0	100.0	98.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00058	906	2309	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00435	487	1677	BCR	0/0	100.0	97.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00040	3213	4346	BLAEC	0/0	100.0	99.9	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00327	2892	3590	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00327	3587	4960	CPXAR	0/0	100.0	99.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00260	2156	2788	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00427	478	1650	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00008	8335	9498	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00427	1777	2307	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00008	6797	8335	EMRY	0/0	100.0	98.8	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00112	2402	4045	EPTA	0/0	100.0	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00008	10533	14126	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00365	1568	2296	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00365	376	1200	GADX	0/0	100.0	97.7	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00448	25	438	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00367	3827	4483	KDPE	0/0	96.9	97.3	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00082	1621	2010	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00082	1173	1607	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00047	13624	14856	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00295	4093	5340	MDTA	0/0	100.0	98.1	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00295	971	4093	MDTB	0/0	100.0	98.4	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00458	1236	2393	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00164	6425	7651	MDTG	0/0	100.0	99.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00083	9270	10478	MDTH	0/0	100.0	98.5	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00291	5063	5392	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00291	4711	5076	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00357	1653	3026	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00390	2061	3293	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00360	3536	4567	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00301	1	1984	MDTO	0/0	96.7	98.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00301	1981	3447	MDTP	0/0	100.0	98.3	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00037	4591	5065	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00034	4736	6484	MSBA	0/0	100.0	99.3	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00027	10413	12314	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00241	3891	5195	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00174	3501	4469	PMRF	0/0	100.0	99.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00063	11897	12766	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00046	8027	8350	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00309	231	1397	UGD	0/0	100.0	95.5	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00446	1273	2916	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Hosp-HIM_071A

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	2698	3534	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00021	3884	4366	dfrA14_5	0/0	100	99.8	DQ388123	dfrA14	Trimethoprim
contig00021	4966	5781	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01133	197	1328	acrE	0/0	97.8	98.5	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig01150	622	1284	acrS	0/0	100.0	97.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00021	2698	3534	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig01389	93	912	bacA	0/0	99.8	97.1	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00053	3396	4118	baeR	0/0	100.0	96.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00353	1924	2556	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00021	3884	4366	dfrA14	0/0	100.0	100.0	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00673	336	1469	Escherichia_coli_ampC	0/0	100.0	97.9	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00008	6303	7607	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00987	403	1495	Escherichia_coli_ampH	0/0	94.4	99.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00647	16	348	Escherichia_coli_emrE	0/0	100.0	91.6	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01283	298	912	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00638	1	713	gadW	0/0	97.8	96.6	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01435	192	1016	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01367	300	683	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00614	154	1401	mdtA	0/0	100.0	96.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00112	571	1728	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00358	720	1946	mdtG	0/0	100.0	98.0	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig01088	7	1239	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00138	449	1480	mdtN	0/0	100.0	97.7	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00138	1480	3531	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00584	810	1284	mphB	0/0	99.6	97.0	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00404	833	1801	pmrF	0/0	100.0	96.3	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00021	4966	5781	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00018	2861	4348	tolC	0/0	100.0	98.3	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00633	441	1945	yojI	0/0	91.5	97.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	2698	3534	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00008	6303	7607	(Bla)AmpC1_Ecoli	0/0	100.0	95.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00673	336	1469	(Bla)AmpC2_Ecoli	0/0	100.0	97.9	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00987	403	1495	(Bla)ampH_Ecoli	0/0	94.4	99.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00145	105	2006	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00021	4966	5781	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00021	3884	4357	(Tmt)dfrA14	0/0	100.0	99.8	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	2698	3534	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00008	6303	7607	(Bla)AmpC1_Ecoli	0/0	100.0	95.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00673	336	1469	(Bla)AmpC2_Ecoli	0/0	100.0	97.9	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00987	403	1495	(Bla)ampH_Ecoli	0/0	94.4	99.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00145	105	2006	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00021	4966	5781	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00021	3884	4357	(Tmt)dfrA14	0/0	100.0	99.8	GU726917:72-545	(Tmt)dfrA14	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01133	197	1328	ACRE	0/0	97.8	98.5	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig01150	622	1284	ACRS	0/0	100.0	97.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00987	403	1495	AMPH	0/0	94.4	99.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00021	2698	3534	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig01389	93	912	BACA	0/0	99.8	97.3	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00053	3396	4118	BAER	0/0	100.0	96.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00348	730	1920	BCR	0/0	100.0	96.4	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00673	336	1469	BLAEC	0/0	100.0	99.2	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00788	370	1068	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00353	1924	2556	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00021	3884	4357	DFRA	0/0	100.0	100.0	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig01444	36	1092	EMRK	0/0	90.8	96.3	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00638	1	713	GADW	0/0	97.8	96.8	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01435	192	1016	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01367	294	683	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00614	154	1401	MDTA	0/0	100.0	96.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00112	571	1728	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00358	720	1946	MDTG	0/0	100.0	98.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig01088	7	1239	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00138	449	1480	MDTN	0/0	100.0	97.7	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00138	1480	3531	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00584	810	1284	MPHB	0/0	99.6	97.0	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00647	16	348	MVRC	0/0	100.0	91.6	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00145	105	2006	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00008	6303	7607	PBP4B	0/0	100.0	95.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00404	833	1801	PMRF	0/0	100.0	96.3	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00096	2844	3713	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig02282	379	673	SOXS	0/0	91.0	98.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00021	4966	5781	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00633	441	1945	YOGI	0/0	91.5	97.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Hosp-HIM_82

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00071	775	1578	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00071	1	775	aph(6)-Id_1	0/0	92.6	100.0	M28829	aph(6)-Id	Streptomycin
contig00111	1903	2376	dfrA5_1	0/0	100.0	99.8	X12868	dfrA5	Trimethoprim
contig00111	539	1405	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00071	1639	2454	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00071	775	1578	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00071	2	775	APH(6)-Id	0/0	92.5	100.0	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00157	2163	2984	bacA	0/0	100.0	99.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00035	1242	1874	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00111	1903	2376	dfrA5	0/0	100.0	99.8	DQ278190:0-474	dfrA5 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00743	162	1334	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig01037	327	1279	emrK	0/0	90.2	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00259	1142	2335	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00042	728	1861	Escherichia_coli_ampC	0/0	100.0	98.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00700	345	959	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00240	668	1396	gadW	0/0	100.0	94.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00419	821	1204	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00358	753	1985	mdtM	0/0	100.0	95.8	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00126	34	2085	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig01213	692	1151	mphB	0/0	96.4	98.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00111	539	1378	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00071	1639	2454	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00527	358	1845	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00071	775	1578	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00071	1	775	(AGly)strB	0/0	92.6	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00042	728	1861	(Bla)AmpC2_Ecoli	0/0	100.0	98.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00111	539	1378	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00071	1639	2454	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00111	1903	2376	(Tmt)dfrA5	0/0	100.0	99.8	X12868:1306-1779	(Tmt)dfrA5	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00071	775	1578	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00071	1	775	(AGly)strB	0/0	92.6	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00042	728	1861	(Bla)AmpC2_Ecoli	0/0	100.0	98.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00111	539	1378	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00071	1639	2454	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00111	1903	2376	(Tmt)dfrA5	0/0	100.0	99.8	X12868:1306-1779	(Tmt)dfrA5	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00259	1142	2335	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00071	775	1602	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00071	1	775	APH6	0/0	92.6	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00371	365	2217	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00157	2163	2984	BACA	0/0	100.0	99.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00042	728	1861	BLAEC	0/0	100.0	98.3	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00409	707	1405	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00035	1242	1874	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00111	1903	2376	DFRA	0/0	100.0	99.8	MEG_2546	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00743	162	1334	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00240	668	1396	GADW	0/0	100.0	99.9	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00419	815	1204	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00419	367	801	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00941	964	1293	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00941	612	977	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00358	753	1985	MDTM	0/0	100.0	95.8	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00126	34	2085	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig01213	692	1151	MPHB	0/0	96.4	98.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00452	1211	2024	ROBA	0/0	93.6	98.9	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00394	951	1273	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00111	412	1379	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00071	1639	2454	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Hosp-KAT_009

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00039	4060	4863	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00039	3224	4060	aph(6)-Id_1	0/0	100	99.9	M28829	aph(6)-Id	Streptomycin
contig00743	580	1089	dfrA8_1	0/0	100	100.0	U10186	dfrA8	Trimethoprim

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00445	1	1043	acrE	0/0	90.1	97.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00039	4060	4863	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00039	3224	4060	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00776	653	1472	bacA	0/0	99.8	94.8	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00533	577	1298	baeR	0/0	99.9	96.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00401	1022	2395	cpxA	0/0	100.0	96.1	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00052	1936	2568	CRP	0/0	100.0	98.9	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00743	580	1089	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig01487	150	764	evgA	0/0	100.0	98.7	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00592	98	826	gadW	0/0	100.0	94.2	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01565	162	950	gadX	0/0	95.6	95.7	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00705	970	1353	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00738	215	1462	mdtA	0/0	100.0	94.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig01017	324	1402	mdtE	0/0	93.2	97.2	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00980	1	1155	mdtM	0/0	93.7	97.8	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00491	1331	1805	mphB	0/0	99.6	96.8	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00422	422	2170	msbA	0/0	100.0	97.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00826	1	737	sul2	0/0	90.3	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00387	351	1838	tolC	0/0	100.0	97.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00039	4060	4863	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00039	3224	4060	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00826	1	737	(Sul)sul2	0/0	90.3	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00743	580	1089	(Tmt)dfrA8	0/0	100.0	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00039	4060	4863	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00039	3224	4060	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00826	1	737	(Sul)sul2	0/0	90.3	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00743	580	1089	(Tmt)dfrA8	0/0	100.0	100.0	U10186:711-1220	(Tmt)dfrA8	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00445	1	1043	ACRE	0/0	90.1	97.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00039	4060	4887	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00039	3224	4060	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00776	653	1472	BACA	0/0	99.8	95.0	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00533	577	1298	BAER	0/0	99.9	96.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00401	327	1025	CPXAR	0/0	100.0	99.0	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00401	1022	2395	CPXAR	0/0	100.0	96.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00052	1936	2568	CRP	0/0	100.0	98.9	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00743	580	1089	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00592	98	826	GADW	0/0	100.0	95.5	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01565	162	950	GADX	0/0	95.6	95.7	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00705	970	1359	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00705	1374	1770	MARR	0/0	91.3	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00738	215	1462	MDTA	0/0	100.0	94.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig01017	324	1402	MDTE	0/0	93.2	97.2	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00328	243	572	MDTI	0/0	100.0	93.9	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00404	651	2024	MDTK	0/0	100.0	97.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00980	1	1155	MDTM	0/0	93.7	97.8	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00491	1331	1805	MPHB	0/0	99.6	96.8	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00422	422	2170	MSBA	0/0	100.0	97.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00440	1427	2280	ROBA	0/0	98.2	97.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig01213	763	1085	SOXS	0/0	99.7	97.2	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00826	1	737	SULII	0/0	90.3	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Hosp-KAT_013

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00038	1270	2073	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00038	434	1270	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00410	1	858	blaTEM-1B_1	0/0	99.7	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00090	2744	3217	dfrA1_10	0/0	100.0	99.8	AF203818	dfrA1	Trimethoprim
contig00090	516	1382	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00038	2134	2949	sul2_3	0/0	100.0	100.0	HQ840942	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00456	816	1973	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00038	1270	2073	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00038	434	1270	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00135	2152	2784	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00090	2744	3217	dfrA1	0/0	100.0	100.0	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00085	1551	2684	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig02179	182	514	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00990	1	614	evgA	0/0	99.8	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00969	1	797	gadX	0/0	96.6	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00148	816	1229	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00060	2447	3604	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00341	243	1454	mdtM	0/0	98.3	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00846	1	1446	mdtP	0/0	98.6	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00090	516	1355	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00038	2134	2949	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00410	1	858	TEM-1	0/0	99.7	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00142	407	1573	ugd	0/0	100.0	97.4	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	1860	2661	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00038	1270	2073	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00038	434	1270	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00085	1551	2684	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00410	1	858	(Bla)blaTEM-105	0/0	99.7	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00090	516	1355	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00038	2134	2949	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig01088	10	660	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00090	2744	3217	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	1860	2661	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00038	1270	2073	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00038	434	1270	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00085	1551	2684	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00410	1	858	(Bla)blaTEM-105	0/0	99.7	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00090	516	1355	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00038	2134	2949	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig01088	10	660	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00090	2744	3217	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00456	816	1973	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00090	1860	2661	ANT3-DPRIME	0/0	96.5	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00038	1270	2097	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00038	434	1270	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00455	216	2068	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00085	1551	2684	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00581	520	1218	CPXAR	0/0	100.0	99.6	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00135	2152	2784	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00090	2744	3217	DFRA	0/0	100.0	99.8	MEG_2528	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00969	1	797	GADX	0/0	96.6	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00148	816	1229	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig02114	154	588	MARR	0/0	100.0	99.1	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00060	2447	3604	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig02382	1	345	MDTJ	0/0	94.3	98.8	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00341	243	1454	MDTM	0/0	98.3	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00846	1	1446	MDTP	0/0	98.6	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig02179	182	514	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00440	230	553	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00090	389	1356	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00038	2134	2949	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00410	1	1225	TEM	0/0	96.6	99.3	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00142	407	1573	UGD	0/0	100.0	97.4	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

Hosp-KAT_023

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00270	826	1629	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00270	1	826	aph(6)-Id_1	0/0	98.7	99.9	M28829	aph(6)-Id	Streptomycin
contig00169	2410	2883	dfrA1_10	0/0	100.0	99.8	AF203818	dfrA1	Trimethoprim
contig00169	182	1048	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00270	1690	2505	sul2_3	0/0	100.0	100.0	HQ840942	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00004	5503	8652	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00270	826	1629	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00270	1	826	APH(6)-Id	0/0	98.7	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig01596	273	994	baeR	0/0	99.9	98.2	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00349	1117	2489	cpxA	0/0	99.9	97.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig01145	649	1281	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00169	2410	2883	dfrA1	0/0	100.0	100.0	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00533	672	1727	emrK	0/0	100.0	97.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig02108	117	647	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	4973	6130	Escherichia_coli_ampH	0/0	100.0	96.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig01113	126	740	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00101	1032	1760	gadW	0/0	100.0	95.8	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00658	1457	1849	H-NS	0/0	94.9	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00793	739	1122	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00439	180	1427	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00266	530	1687	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00596	1	1201	mdtG	0/0	97.9	97.8	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00505	597	1805	mdtH	0/0	100.0	98.2	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00485	734	1966	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00381	1	2008	mdtO	0/0	97.9	96.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00033	277	753	mphB	0/0	100.0	97.9	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00169	182	1021	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00270	1690	2505	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00324	469	1956	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00169	1526	2327	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00270	826	1629	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00270	1	826	(AGly)strB	0/0	98.7	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00002	4973	6130	(Bla)ampH_Ecoli	0/0	100.0	96.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00169	182	1021	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00270	1690	2505	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00169	2410	2883	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00169	1526	2327	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00270	826	1629	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00270	1	826	(AGly)strB	0/0	98.7	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00002	4973	6130	(Bla)ampH_Ecoli	0/0	100.0	96.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00169	182	1021	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00270	1690	2505	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00169	2410	2883	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00004	5503	8652	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	4973	6130	AMPH	0/0	100.0	96.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00169	1526	2327	ANT3-DPRIME	0/0	96.5	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00270	826	1653	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00270	1	826	APH6	0/0	98.7	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig01596	273	994	BAER	0/0	99.9	98.2	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00349	422	1120	CPXAR	0/0	100.0	99.6	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00349	1117	2489	CPXAR	0/0	99.9	98.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig01145	649	1281	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00169	2410	2883	DFRA	0/0	100.0	99.8	MEG_2528	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00533	672	1835	EMRK	0/0	100.0	97.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig02108	117	647	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00101	1032	1760	GADW	0/0	100.0	97.4	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00658	1457	1849	HNS	0/0	94.9	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00793	733	1122	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00793	285	719	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00439	180	1427	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00266	530	1687	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00596	1	1201	MDTG	0/0	97.9	98.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00505	597	1805	MDTH	0/0	100.0	98.2	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig01603	1	306	MDTI	0/0	92.7	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig01603	293	658	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00485	734	1966	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00381	1	2008	MDTO	0/0	97.9	96.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00033	277	753	MPHB	0/0	100.0	97.9	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00450	828	1697	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig01014	67	389	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00169	55	1022	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00270	1690	2505	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

Hosp-KAT_039

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00088	3942	4802	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00839	236	1495	cmlA1_1	0/0	100.0	99.8	M64556	cmlA1	Chloramphenicol
contig01298	683	1180	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00016	1123	1914	sul3_2	0/0	100.0	99.9	AJ459418	sul3	Sulfamethoxazole
contig00228	1476	2722	tet(A)_6	0/0	97.8	99.9	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00309	145	3063	acrB	0/0	92.7	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00198	30	851	bacA	0/0	100.0	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00617	193	915	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00839	236	1495	cmlA1	0/0	100.0	99.8	M64556.1:600-1860	cmlA1 is a plasmid or transposon-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa and Klebsiella pneumoniae	phenicol
contig00086	3577	4950	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00389	995	1627	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01298	683	1180	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00331	122	1294	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00331	1311	2849	emrB	0/0	100.0	98.8	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00147	704	1759	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00006	2390	4033	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00640	208	1401	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00907	591	1655	Escherichia_coli_ampC	0/0	93.9	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00618	145	1449	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00373	1283	2440	Escherichia_coli_ampH	0/0	100.0	98.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00109	1761	2093	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00147	2283	2897	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig01782	86	499	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00452	1532	1915	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00764	117	1364	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00346	571	1728	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00571	296	1528	mdtM	0/0	100.0	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00189	70	1818	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig02346	23	355	qacH	0/0	100.0	91.6	DQ149925.1:188-521	qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae	fluoroquinolone
contig00016	1123	1914	sul3	0/0	100.0	99.9	FJ196385:9323-8531	Sul3 is a sulfonamide resistant dihydropteroate synthase similar to Sul1 and Sul2. Its resistance gene was found encoded in E. coli plasmid DNA of sulfonamide resistant isolates.	sulfonamide
contig00088	3942	4802	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00228	1476	2722	tet(A)	0/0	97.8	99.9	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00005	3313	4800	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00618	145	1449	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00907	591	1655	(Bla)AmpC2_Ecoli	0/0	93.9	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00373	1283	2440	(Bla)ampH_Ecoli	0/0	100.0	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00088	3942	4802	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00069	1969	3870	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00839	236	1495	(Phe)cmlA1	0/0	100.0	99.8	M64556:601-1860	(Phe)cmlA1	NA
contig00016	1123	1914	(Sul)sul3	0/0	100.0	99.9	HQ875016:7396-8187	(Sul)sul3	NA
contig00228	1448	2722	(Tet)tetA	0/0	100.0	99.9	JX424423:94438-95712	(Tet)tetA	NA
contig00228	2753	3403	(Tet)tetR	0/0	100.0	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig01298	683	1180	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00618	145	1449	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00907	591	1655	(Bla)AmpC2_Ecoli	0/0	93.9	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00373	1283	2440	(Bla)ampH_Ecoli	0/0	100.0	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00088	3942	4802	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00069	1969	3870	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00839	236	1495	(Phe)cmlA1	0/0	100.0	99.8	M64556:601-1860	(Phe)cmlA1	NA
contig00016	1123	1914	(Sul)sul3	0/0	100.0	99.9	HQ875016:7396-8187	(Sul)sul3	NA
contig00228	1448	2722	(Tet)tetA	0/0	100.0	99.9	JX424423:94438-95712	(Tet)tetA	NA
contig00228	2753	3403	(Tet)tetR	0/0	100.0	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig01298	683	1180	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00640	208	1401	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00309	145	3063	ACRB	0/0	92.7	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00373	1283	2440	AMPH	0/0	100.0	98.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00789	1	1834	ASMA	0/0	98.9	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00198	30	851	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00617	193	915	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00540	1	1116	BCR	0/0	98.4	96.5	MEG_1209	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00907	591	1655	BLAEC	0/0	93.9	100.0	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00839	35	1495	CMLA	1/1	100.0	99.7	MEG_1768	Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:CMLA	NA
contig00086	2882	3580	CPXAR	0/0	100.0	99.6	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00086	3577	4950	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00389	995	1627	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00796	1	872	CTX	0/0	98.1	95.3	MEG_2430	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig01298	683	1180	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00331	122	1294	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00331	1311	2849	EMRB	0/0	100.0	98.8	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00147	704	1867	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00006	2390	4033	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01782	86	499	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00452	1526	1915	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00452	1078	1512	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00764	117	1364	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00346	571	1728	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig01876	130	495	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00571	296	1528	MDTM	0/0	100.0	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00189	70	1818	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00109	1761	2093	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00069	1969	3870	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00618	145	1449	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig02346	23	355	QACL	0/0	100.0	100.0	MEG_5852	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACL	NA
contig00561	292	1161	ROBA	0/0	100.0	99.4	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00610	1843	2166	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00016	1123	1914	SULIII	0/0	100.0	99.9	MEG_6639	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULIII	NA
contig00088	3575	4820	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00228	1448	2722	TETA	0/0	100.0	99.9	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA

Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample

Select the database

Resfinder

CARD

ARG-ANNOT

NCBI

MEGARES

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Plasmid Profiling

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Catt-BWE_048B

## [1] "NO PLASMID FOUND!!"

Catt-BWE_054A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00031	5673	5814	IncI1_1_Alpha	0/0	100	99.3	AP005147	IncI1_1_Alpha_AP005147

Catt-BWE_113B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00150	3342	3729	IncFIA_1	0/0	100	100.0	AP001918	IncFIA_1__AP001918
contig00087	1891	2572	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00028	3737	3878	IncI1_1_Alpha	0/0	100	100.0	AP005147	IncI1_1_Alpha_AP005147

Catt-HIM_031B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00874	452	712	IncFII(pRSB107)_1_pRSB107	0/0	100	100	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

Catt-HIM_045B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00024	593	1274	IncFIB(AP001918)_1	0/0	100	97.7	AP001918	IncFIB(AP001918)_1__AP001918

Catt-HIM_048B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01949	1	485	IncHI1B(CIT)_1_pNDM-CIT	0/0	90.2	92.8	JX182975	IncHI1B(CIT)_1_pNDM-CIT_JX182975
contig00432	1416	2300	p0111_1	0/0	100.0	98.5	AP010962	p0111_1__AP010962

Catt-HIM_068A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig02025	68	328	IncFII_1	0/0	100	97.7	AY458016	IncFII_1__AY458016

Catt-HIM_073A

## [1] "NO PLASMID FOUND!!"

Catt-HIM_082A1

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01904	68	328	IncFII_1	0/0	100	97.7	AY458016	IncFII_1__AY458016

Catt-KAT_009_A1

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00411	2272	2953	IncFIB(AP001918)_1	0/0	100	98.2	AP001918	IncFIB(AP001918)_1__AP001918

Catt-KAT_013A1

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00152	41	428	IncFIA_1	0/0	100	100.0	AP001918	IncFIA_1__AP001918
contig00005	4677	5358	IncFIB(AP001918)_1	0/0	100	98.5	AP001918	IncFIB(AP001918)_1__AP001918

Catt-KAT_036B

## [1] "NO PLASMID FOUND!!"

Home-BWE_054A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00037	5978	6659	IncFIB(AP001918)_1	0/0	100	97.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00027	8857	9117	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

Home-HIM_031A

## [1] "NO PLASMID FOUND!!"

Home-HIM_032A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00049	1589	2270	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

Home-HIM_045A

## [1] "NO PLASMID FOUND!!"

Home-HIM_047B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00229	3240	3986	IncFII(pECLA)_1_pECLA	0/0	100	96.2	CP001919	IncFII(pECLA)_1_pECLA_CP001919

Home-HIM_048A

## [1] "NO PLASMID FOUND!!"

Home-HIM_068B

## [1] "NO PLASMID FOUND!!"

Home-HIM_071A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00001	10913	11594	IncFIB(AP001918)_1	0/0	100	99.6	AP001918	IncFIB(AP001918)_1__AP001918

Home-HIM_072A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00153	1170	1851	IncFIB(AP001918)_1	0/0	100	98.7	AP001918	IncFIB(AP001918)_1__AP001918
contig00086	2974	3234	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

Home-HIM_073B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00009	685	838	Col156_1	0/0	100	98.7	NC_009781	Col156_1__NC_009781
contig00049	2274	2955	IncFIB(AP001918)_1	0/0	100	96.6	AP001918	IncFIB(AP001918)_1__AP001918
contig00197	1122	1380	IncFII(29)_1_pUTI89	0/0	100	100.0	CP003035	IncFII(29)_1_pUTI89_CP003035

Home-HIM_075A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00322	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

Home-HIM_82A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00093	4747	4897	IncB/O/K/Z_1	2/2	99.3	98.0	CU928147	IncB/O/K/Z_1__CU928147
contig00343	779	1460	IncFIB(AP001918)_1	0/0	100.0	97.2	AP001918	IncFIB(AP001918)_1__AP001918

Home-KAT_009A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00175	1709	1818	Col440I_1	0/0	96.5	96.4	CP023920.1	Col440I_1__CP023920.1
contig01726	486	848	IncFIA_1	0/0	93.6	99.2	AP001918	IncFIA_1__AP001918
contig00340	763	1444	IncFIB(AP001918)_1	0/0	100.0	97.5	AP001918	IncFIB(AP001918)_1__AP001918

Home-KAT_013A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00019	3211	3362	Col156_1	0/0	98.7	95.4	NC_009781	Col156_1__NC_009781

Home-KAT_023A

## [1] "NO PLASMID FOUND!!"

Home-KAT_039B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00879	526	945	IncHI1A_1	0/0	100	100	AF250878	IncHI1A_1__AF250878
contig00001	19858	20852	pSL483_1	0/0	100	93	CP001137	pSL483_1__CP001137

Hosp-BWE_048

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00554	288	549	Col(MG828)_1	0/0	100	92.0	NC_008486	Col(MG828)_1__NC_008486
contig00718	484	1165	IncFIB(AP001918)_1	0/0	100	95.3	AP001918	IncFIB(AP001918)_1__AP001918

Hosp-BWE_054

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00111	1273	1414	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00049	1679	2360	IncFIB(AP001918)_1	0/0	100.0	96.6	AP001918	IncFIB(AP001918)_1__AP001918
contig00016	3322	3580	IncFII(29)_1_pUTI89	0/0	100.0	99.6	CP003035	IncFII(29)_1_pUTI89_CP003035
contig00006	7317	8081	IncY_1	0/0	100.0	99.9	K02380	IncY_1__K02380

Hosp-BWE_076

## [1] "NO PLASMID FOUND!!"

Hosp-BWE_106

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00001	3365	3748	IncFIA_1	0/0	99.0	100.0	AP001918	IncFIA_1__AP001918
contig00027	564	1245	IncFIB(AP001918)_1	0/0	100.0	97.8	AP001918	IncFIB(AP001918)_1__AP001918
contig00011	1600	2096	IncFIC(FII)_1	1/2	99.6	95.6	AP001918	IncFIC(FII)_1__AP001918

Hosp-HIM_031

## [1] "NO PLASMID FOUND!!"

Hosp-HIM_045

## [1] "NO PLASMID FOUND!!"

Hosp-HIM_048

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00003	12699	13380	IncFIB(AP001918)_1	0/0	100	99.3	AP001918	IncFIB(AP001918)_1__AP001918

Hosp-HIM_068

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00024	10697	11461	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

Hosp-HIM_071A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01233	359	512	Col156_1	0/0	100	98.7	NC_009781	Col156_1__NC_009781
contig00087	2156	2837	IncFIB(AP001918)_1	0/0	100	96.6	AP001918	IncFIB(AP001918)_1__AP001918
contig00001	10360	10618	IncFII(29)_1_pUTI89	0/0	100	100.0	CP003035	IncFII(29)_1_pUTI89_CP003035

Hosp-HIM_82

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00011	4050	4163	Col440I_1	0/0	100.0	94.7	CP023920.1	Col440I_1__CP023920.1
contig00512	1576	1730	IncB/O/K/Z_2	1/1	96.2	96.1	GU256641	IncB/O/K/Z_2__GU256641

Hosp-KAT_009

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00249	1371	1484	Col440I_1	0/0	100	94.7	CP023920.1	Col440I_1__CP023920.1
contig00048	2262	2943	IncFIB(AP001918)_1	0/0	100	96.8	AP001918	IncFIB(AP001918)_1__AP001918

Hosp-KAT_013

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00035	1832	2513	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

Hosp-KAT_023

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00011	3365	3752	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00032	1858	2539	IncFIB(AP001918)_1	0/0	100	97.7	AP001918	IncFIB(AP001918)_1__AP001918
contig00020	4419	4679	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

Hosp-KAT_039

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00066	4509	4759	IncR_1	0/0	100	100	DQ449578	IncR_1__DQ449578

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Catt-BWE_048B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00811	567	1424	entB	0/0	100.0	97.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01448	1	915	fepB	0/0	95.6	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00635	750	1940	fes	0/0	99.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00029	5052	5656	fimA	1/1	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00029	3686	4411	fimC	0/0	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00029	983	3619	fimD	0/0	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00029	443	976	fimF	0/0	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01450	70	978	fimH	0/0	99.7	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00029	4448	4987	fimI	0/0	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00321	1535	2365	gspC	0/0	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00572	210	740	gspH	0/0	100.0	95.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00572	737	1108	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00572	1141	1710	gspJ	0/0	100.0	96.5	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00019	167	1027	gspL	0/0	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00019	1143	1565	gspM	0/0	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01138	182	1234	ompA	1/12	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00733	555	1308	yagV/ecpE	0/0	99.7	96.7	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00208	2441	3109	yagY/ecpB	0/0	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00208	1796	2383	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00208	1131	1721	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-BWE_054A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00272	680	1708	chuS	0/0	100.0	97.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00409	326	1318	chuU	0/0	100.0	99.0	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00409	1285	2085	chuV	0/0	100.0	98.1	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00425	468	1805	chuW	0/0	100.0	96.7	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00273	1204	1950	entA	0/0	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00273	347	1204	entB	0/0	100.0	98.5	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00344	1	2014	espL4	0/0	92.1	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00066	122	4372	fdeC	0/0	100.0	94.8	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00395	9	1025	fepD	0/0	100.0	95.6	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00395	1022	2014	fepG	0/0	100.0	95.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00789	600	1802	fes	0/0	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig01269	490	1095	fimA	0/0	100.0	90.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01910	3	605	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00224	2609	3334	fimC	0/0	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00224	1	2543	fimD	0/0	96.4	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01895	299	757	fimG	0/0	91.1	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01560	70	981	fimH	0/0	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00487	700	1530	gspC	0/0	100.0	94.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00280	1133	2626	gspE	0/0	100.0	94.3	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00441	457	912	gspG	0/0	100.0	96.7	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00441	949	1479	gspH	0/0	100.0	96.4	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00441	1476	1847	gspI	0/0	100.0	93.5	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00441	1880	2449	gspJ	0/0	100.0	96.0	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00650	850	1272	gspM	0/0	100.0	97.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00949	215	1255	ompA	0/0	100.0	98.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00425	1818	2312	shuX	0/0	100.0	95.8	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00639	1364	2032	yagY/ecpB	0/0	100.0	98.4	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00639	719	1306	yagZ/ecpA	0/0	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00639	54	644	ykgK/ecpR	0/0	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-BWE_113B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01089	316	1173	entB	0/0	100.0	97.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	5480	7818	faeD	0/0	95.9	91.4	YP_002295985	(faeD) fimbrial usher protein FaeD [K88 pili/F4 fimbriae (AI040)] [Escherichia coli SE11]
contig00485	47	862	fepC	0/0	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00429	326	1528	fes	0/0	100.0	96.4	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00696	1406	2011	fimA	0/0	100.0	90.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00696	40	765	fimC	0/0	100.0	98.1	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00139	2018	4588	fimD	0/0	97.5	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01967	1	590	fimE	0/0	98.8	98.6	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00139	1478	2011	fimF	0/0	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00139	962	1465	fimG	0/0	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00139	40	951	fimH	0/0	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00696	802	1341	fimI	0/0	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00417	1	1792	gspD	1/15	96.8	96.9	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00149	2965	3420	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00149	2398	2928	gspH	0/0	100.0	95.3	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00149	2030	2401	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00149	1428	1997	gspJ	0/0	100.0	97.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00149	454	1431	gspK	0/0	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02005	103	525	gspM	0/0	100.0	93.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00945	303	1343	ompA	0/0	100.0	98.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00749	1024	1777	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00045	5576	6244	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00045	4931	5518	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00045	4266	4856	ykgK/ecpR	0/0	100.0	97.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-HIM_031B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00004	1062	1178	astA	0/0	100.0	98.3	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig01377	150	719	espY2	0/0	100.0	94.4	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01066	109	703	fimE	0/0	99.7	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00119	309	812	fimG	0/0	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00119	823	1734	fimH	0/0	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00435	499	1038	fimI	0/0	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00083	894	1724	gspC	0/0	100.0	94.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00446	381	752	gspI	0/0	100.0	96.0	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00187	525	887	gtrA	0/0	100.0	90.1	NP_706257	(gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00623	1	775	kpsM	0/0	99.7	94.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig01126	110	697	yagZ/ecpA	0/0	100.0	98.8	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-HIM_045B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01774	170	286	astA	0/0	100	96.6	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig01134	139	996	entB	0/0	100	97.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01018	500	1102	fimB	0/0	100	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	1488	2021	fimF	0/0	100	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	972	1475	fimG	0/0	100	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	50	961	fimH	0/0	100	97.8	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00532	638	1177	fimI	0/0	100	97.8	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	2300	5296	hlyA	0/0	100	98.4	YP_325608	(hlyA) hemolysin toxin protein [Hemolysin (VF0207)] [Escherichia coli O157:H7 str. EDL933]
contig00002	130	2250	hlyB	0/0	100	99.2	YP_325609	(hlyB) hemolysin transport protein [Hemolysin (VF0207)] [Escherichia coli O157:H7 str. EDL933]
contig00002	5298	5813	hlyC	0/0	100	97.1	YP_325607	(hlyC) hemolysin transport protein [Hemolysin (VF0207)] [Escherichia coli O157:H7 str. EDL933]
contig00038	1657	2697	ompA	0/0	100	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00548	378	1337	stx2A	0/0	100	98.3	NP_286976	(stx2A) shiga-like toxin II A subunit encoded by bacteriophage BP-933W [Stx (VF0206)] [Escherichia coli O157:H7 str. EDL933]
contig00548	97	366	stx2B	0/0	100	96.7	NP_286977	(stx2B) shiga-like toxin II B subunit encoded by bacteriophage BP-933W [Stx (VF0206)] [Escherichia coli O157:H7 str. EDL933]
contig00188	1629	2297	yagY/ecpB	0/0	100	98.4	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00188	983	1570	yagZ/ecpA	0/0	100	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00188	318	908	ykgK/ecpR	0/0	100	97.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-HIM_048B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00834	45	1473	aslA	1/1	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00351	436	1182	entA	0/0	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00616	253	1440	entC	0/0	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00568	1033	1848	fepC	0/0	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00544	692	1708	fepD	0/0	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01481	206	811	fimA	0/0	100.0	90.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01878	1	592	fimB	0/0	98.2	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	4751	5476	fimC	0/0	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	2048	4684	fimD	0/0	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	1508	2041	fimF	0/0	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	992	1495	fimG	0/0	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	70	981	fimH	0/0	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	500	1330	gspC	0/0	100.0	95.4	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00058	1570	3420	gspD	1/15	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00058	3420	4913	gspE	0/0	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01861	200	636	gspG	0/0	95.8	94.7	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01714	187	558	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00724	23	883	gspL	0/0	100.0	97.2	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02101	103	490	gspM	0/0	91.7	97.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00787	413	1453	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

Catt-HIM_068A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01075	459	1205	entA	0/0	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01095	1	1143	entC	0/0	96.2	97.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01474	1	928	fepB	0/0	97.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00434	1213	2028	fepC	0/0	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01489	386	976	fimA	1/1	97.5	90.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00566	406	909	fimG	0/0	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00566	920	1831	fimH	0/0	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00963	326	1156	gspC	0/0	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00088	330	1823	gspE	0/0	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00088	1823	3022	gspF	0/0	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00088	3063	3518	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01337	118	687	gspJ	0/0	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02122	93	515	gspM	0/0	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01152	154	1206	ompA	1/12	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00142	779	1447	yagY/ecpB	0/0	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00142	134	721	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-HIM_073A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01620	142	823	entA	0/0	91.3	95.5	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01918	74	679	fimA	0/0	100.0	90.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01743	194	780	fimB	0/0	97.3	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00462	786	1511	fimC	0/0	100.0	98.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00488	943	1476	fimF	0/0	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00488	427	930	fimG	0/0	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00139	1787	2356	gspJ	0/0	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00139	813	1790	gspK	0/0	100.0	97.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00063	1366	2034	yagY/ecpB	0/0	100.0	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00063	721	1308	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00063	56	646	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-HIM_082A1

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00668	795	1541	entA	0/0	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00668	1	795	entB	0/0	92.7	97.6	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00539	1025	2275	entS	0/0	100.0	95.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00539	65	1021	fepB	0/0	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00494	725	1927	fes	0/0	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig02179	1	550	fimA	1/1	90.8	90.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01682	242	844	fimB	0/0	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01023	223	948	fimC	0/0	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00415	319	852	fimF	0/0	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01403	50	961	fimH	0/0	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01023	985	1524	fimI	0/0	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00212	775	1605	gspC	0/0	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00212	1845	3648	gspD	1/15	97.4	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00173	1	1448	gspE	0/0	96.9	97.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00173	1448	2647	gspF	0/0	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00173	2688	3143	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00173	3180	3710	gspH	0/0	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01267	301	1054	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00396	1	2330	yagX/ecpC	0/0	92.2	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01851	51	641	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-KAT_009_A1

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00761	247	1675	aslA	1/1	100.0	92.7	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00297	3931	4677	entA	0/0	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00297	3074	3931	entB	0/0	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00297	253	1440	entC	0/0	100.0	97.8	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00297	1450	3060	entE	0/0	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00720	39	1289	entS	0/0	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00634	169	2409	fepA	0/0	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00437	1571	2386	fepC	0/0	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00437	2383	3375	fepG	0/0	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00513	23	1225	fes	0/0	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig01083	234	836	fimB	0/0	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00188	4090	4815	fimC	0/0	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00188	1387	4023	fimD	0/0	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01187	1	580	fimE	0/0	97.2	99.5	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00188	847	1380	fimF	0/0	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00188	331	834	fimG	0/0	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00188	4852	5391	fimI	0/0	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00306	653	2503	gspD	1/15	100.0	96.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00306	2503	3996	gspE	0/0	100.0	95.6	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00616	1876	2331	gspG	0/0	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00616	1309	1839	gspH	0/0	100.0	96.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00616	941	1312	gspI	0/0	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00616	339	908	gspJ	0/0	100.0	94.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00752	193	1053	gspL	0/0	100.0	95.2	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00799	725	1501	kpsM	0/0	100.0	95.0	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00530	1006	2046	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00280	837	1590	yagV/ecpE	0/0	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00255	2055	4580	yagX/ecpC	0/0	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00255	1361	2029	yagY/ecpB	0/0	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00255	716	1303	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00255	51	641	ykgK/ecpR	0/0	100.0	97.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-KAT_013A1

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00228	125	2365	fepA	0/0	100.0	97.6	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00886	27	530	fimG	0/0	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01120	156	986	gspC	0/0	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00175	38	1888	gspD	1/15	100.0	97.6	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00117	665	1864	gspF	0/0	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00117	1905	2360	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00117	2397	2927	gspH	0/0	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00200	1722	2291	gspJ	0/0	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00200	748	1725	gspK	0/0	100.0	97.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00190	1577	2330	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00190	10	1653	yagW/ecpD	0/0	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00726	688	1356	yagY/ecpB	0/0	100.0	98.2	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00726	43	630	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Catt-KAT_036B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00139	286	819	fimF	0/0	100	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00401	21	392	gspI	0/0	100	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]

Home-BWE_054A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00577	1	2446	aggC	0/0	96.7	99.7	AAA57452	(aggC) usher protein [AAFs (VF0214)] [Escherichia coli 17-2]
contig00825	1118	1234	astA	0/0	100.0	98.3	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00141	1640	2632	chuU	0/0	100.0	98.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00141	873	1673	chuV	0/0	100.0	98.9	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00141	3811	5148	chuW	0/0	100.0	96.7	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00141	2681	3304	chuY	0/0	100.0	97.0	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00579	1393	2250	entB	0/0	100.0	97.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00664	516	2414	espL1	0/0	100.0	96.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00424	98	667	espY2	0/0	100.0	94.4	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01061	654	1431	fepC	0/0	95.3	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00718	837	1853	fepD	0/0	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00666	479	1681	fes	0/0	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00669	1727	2332	fimA	0/0	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01052	790	1391	fimB	1/1	99.8	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00669	361	1086	fimC	0/0	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01311	171	765	fimE	0/0	99.7	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01014	32	535	fimG	0/0	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01014	546	1457	fimH	0/0	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00669	1123	1662	fimI	0/0	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00107	1511	2341	gspC	0/0	100.0	94.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00107	2581	4431	gspD	1/15	100.0	95.4	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00107	4431	5924	gspE	0/0	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00399	115	570	gspG	0/0	100.0	97.8	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00399	607	1137	gspH	0/0	100.0	95.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00399	1134	1505	gspI	0/0	100.0	96.0	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00399	1538	2107	gspJ	0/0	100.0	95.3	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00399	2104	3081	gspK	0/0	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01345	444	853	gspM	0/0	96.9	97.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01015	511	873	gtrA	0/0	100.0	90.1	NP_706257	(gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00541	1	1586	kpsD	0/0	94.6	96.9	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00917	626	1402	kpsM	0/0	100.0	94.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00071	1015	2055	ompA	0/0	100.0	98.9	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00327	1160	2188	shuS	0/0	100.0	96.5	YP_405020	(shuS) heme/hemoglobin transport protein ShuS [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00141	3304	3798	shuX	0/0	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00215	856	1609	yagV/ecpE	0/0	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00468	1031	1699	yagY/ecpB	0/0	100.0	98.4	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00468	386	973	yagZ/ecpA	0/0	100.0	98.8	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_031A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00347	1563	2813	entS	0/0	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00083	2562	4460	espL1	0/0	100.0	94.9	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00153	278	4503	fdeC	1/3	99.4	91.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00347	603	1559	fepB	0/0	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00745	794	1609	fepC	0/0	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01602	208	810	fimB	0/0	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00552	343	1068	fimC	0/0	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00175	1488	2021	fimF	0/0	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00175	972	1475	fimG	0/0	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00175	50	961	fimH	0/0	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00552	1105	1644	fimI	0/0	100.0	97.6	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00433	1535	2365	gspC	0/0	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00567	200	655	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00567	692	1222	gspH	0/0	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00567	1219	1590	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00567	1623	2192	gspJ	0/0	100.0	97.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01929	103	525	gspM	0/0	100.0	93.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00382	56	1096	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00108	1461	2214	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00108	1	1537	yagW/ecpD	0/0	93.5	98.8	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00080	3997	4665	yagY/ecpB	0/0	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00080	3352	3939	yagZ/ecpA	0/0	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00080	2687	3277	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_032A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00831	996	1598	fimB	0/0	100.0	97.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00203	1	2453	fimD	0/0	93.0	98.4	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01733	259	792	fimF	0/0	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01265	222	1133	fimH	0/0	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00888	68	607	fimI	0/0	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00695	92	922	gspC	0/0	100.0	96.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00115	1161	2360	gspF	0/0	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00115	2401	2856	gspG	0/0	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00115	2893	3423	gspH	0/0	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00115	3420	3788	gspI	0/0	99.2	95.1	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02063	1	556	gspJ	0/0	97.5	96.8	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01302	640	1062	gspM	0/0	100.0	94.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01247	350	1103	yagV/ecpE	0/0	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00736	24	692	yagY/ecpB	0/0	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01011	830	1398	yagZ/ecpA	0/0	96.8	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01011	165	755	ykgK/ecpR	0/0	100.0	97.1	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_045A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00840	1047	1750	entA	0/0	94.2	96.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00507	588	2198	entE	0/0	100.0	95.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	1	1214	espX5	1/12	93.0	94.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00647	133	2373	fepA	0/0	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00916	496	1452	fepB	0/0	100.0	97.3	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00401	759	1775	fepD	0/0	100.0	95.7	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00401	1772	2764	fepG	0/0	100.0	94.6	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00715	869	2071	fes	0/0	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig01265	221	823	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00444	786	1511	fimC	0/0	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00806	370	873	fimG	0/0	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00806	884	1795	fimH	0/0	100.0	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00444	1548	2087	fimI	0/0	100.0	97.8	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	9031	9861	gspC	0/0	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	6941	8791	gspD	1/15	100.0	97.3	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	5448	6941	gspE	0/0	100.0	96.2	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	4249	5448	gspF	0/0	100.0	96.3	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	3753	4208	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	3186	3716	gspH	0/0	100.0	95.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	2818	3189	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	2216	2785	gspJ	0/0	100.0	96.5	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	1242	2219	gspK	0/0	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	67	927	gspL	0/0	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01499	103	518	gspM	0/0	98.3	94.0	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00562	15	1067	ompA	1/12	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00206	950	1703	yagV/ecpE	0/0	99.7	96.7	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	7636	10161	yagX/ecpC	0/0	100.0	98.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	6942	7610	yagY/ecpB	0/0	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	6297	6884	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00703	599	2176	ybtE	0/0	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00238	1606	2910	ybtS	0/0	100.0	97.5	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00156	4921	6021	ybtU	0/0	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00238	2938	4218	ybtX	0/0	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	5632	6222	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_047B

## [1] "NO VIRULENCE FACTORS DETECTED!!!"

Home-HIM_048A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00512	53	1481	aslA	1/1	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00331	2261	4207	chuA	0/0	100.0	99.7	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00331	1184	2212	chuS	0/0	100.0	99.3	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00414	107	1099	chuT	0/0	100.0	99.7	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00540	1614	2414	chuV	0/0	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00414	1119	2456	chuW	0/0	100.0	99.4	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00414	2469	2963	chuX	0/0	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00414	2963	3586	chuY	0/0	100.0	99.5	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00083	6631	7488	entB	0/0	100.0	99.3	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00083	3810	4997	entC	0/0	100.0	99.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00083	5007	6617	entE	0/0	100.0	98.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00247	1443	5296	entF	0/0	99.3	98.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00083	1423	2673	entS	0/0	100.0	97.9	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00062	2793	7043	fdeC	0/0	100.0	99.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00655	125	2365	fepA	0/0	100.0	99.5	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00083	2677	3633	fepB	0/0	100.0	99.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00603	1232	2047	fepC	0/0	100.0	99.0	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00083	308	1324	fepD	0/0	100.0	98.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00247	23	1225	fes	0/0	100.0	99.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00377	3142	3747	fimA	0/0	100.0	91.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01154	183	775	fimB	0/0	98.3	99.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00377	1776	2501	fimC	0/0	100.0	99.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00554	1514	2047	fimF	0/0	100.0	98.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00554	998	1501	fimG	0/0	100.0	99.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00554	76	987	fimH	0/0	100.0	99.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00377	2538	3077	fimI	0/0	100.0	99.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00622	519	2369	gspD	1/15	100.0	94.7	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00451	2025	2480	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00451	1458	1988	gspH	0/0	100.0	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00451	1090	1461	gspI	0/0	100.0	91.4	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00451	488	1057	gspJ	0/0	100.0	94.6	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00741	542	1402	gspL	0/0	100.0	95.5	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00741	5	426	gspM	0/0	99.8	93.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00317	1668	3038	ibeA	2/2	99.9	98.5	AAF98391	(ibeA) invasion protein IbeA [Ibes (VF0237)] [Escherichia coli O18:K1:H7 str. RS218]
contig00082	2448	4124	kpsD	0/0	100.0	99.2	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00681	606	1382	kpsM	0/0	100.0	95.2	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00941	15	1055	ompA	0/0	100.0	99.6	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00152	2749	3502	yagV/ecpE	0/0	99.7	98.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00152	1182	2825	yagW/ecpD	0/0	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00452	1532	2200	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00452	888	1475	yagZ/ecpA	0/0	100.0	98.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00515	1215	2018	ybtT	0/0	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00515	2015	3115	ybtU	0/0	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00607	380	1660	ybtX	0/0	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00452	224	814	ykgK/ecpR	0/0	100.0	99.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_068B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00758	1	1380	aslA	1/1	96.6	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00931	439	1395	fepB	0/0	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00311	898	2100	fes	0/0	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00884	690	1295	fimA	0/0	100.0	92.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00906	692	1294	fimB	0/0	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00426	1508	2041	fimF	0/0	100.0	97.0	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00426	992	1495	fimG	0/0	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00426	70	981	fimH	0/0	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00884	86	625	fimI	0/0	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00076	177	2027	gspD	1/15	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00076	2027	3520	gspE	0/0	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00775	154	609	gspG	0/0	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00775	646	1176	gspH	0/0	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00775	1173	1544	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00928	1	823	gspL	0/0	95.6	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00928	939	1361	gspM	0/0	100.0	97.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00304	1164	2204	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig01129	4	757	yagV/ecpE	0/0	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00100	734	1402	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00100	89	676	yagZ/ecpA	0/0	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_071A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00795	41	1469	aslA	1/1	100.0	94.0	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00355	891	2228	chuW	0/0	100.0	96.3	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig01641	26	775	espY1	1/3	99.6	95.6	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00728	684	1499	fepC	0/0	100.0	96.9	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00558	991	2183	fes	0/0	99.2	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00019	6099	6704	fimA	0/0	100.0	96.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	4733	5458	fimC	0/0	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	2030	4666	fimD	0/0	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	1490	2023	fimF	0/0	100.0	96.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	974	1477	fimG	0/0	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	52	963	fimH	0/0	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	5495	6034	fimI	0/0	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00591	278	2112	gspD	1/15	99.1	97.5	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00854	189	1637	gspE	0/0	97.0	97.8	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	3396	3851	gspG	0/0	100.0	96.7	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	2829	3359	gspH	0/0	100.0	97.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	2461	2832	gspI	0/0	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	1859	2428	gspJ	0/0	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	885	1862	gspK	0/0	100.0	96.3	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01914	325	726	gspM	0/0	95.0	95.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00491	1639	2334	shuV	0/0	90.3	98.8	YP_405013	(shuV) ATP-binding component of hemin transport system [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00355	2241	2735	shuX	0/0	100.0	98.2	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig01176	337	1092	yagV/ecpE	0/0	100.0	98.3	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01169	326	994	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01496	80	670	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_072A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01102	917	1313	agg3B	0/0	90.0	99.8	AAM88297	(agg3B) invasin protein [AAFs (VF0214)] [Escherichia coli 55989]
contig01774	551	667	astA	0/0	100.0	100.0	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00143	1183	1929	entA	0/0	100.0	95.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00143	326	1183	entB	0/0	100.0	97.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00494	243	1430	entC	0/0	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00773	241	1491	entS	0/0	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00408	845	1660	fepC	0/0	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00951	185	1015	gspC	0/0	100.0	94.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	4919	6412	gspE	0/0	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	3720	4919	gspF	0/0	100.0	96.3	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	3224	3679	gspG	0/0	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	2657	3187	gspH	0/0	100.0	95.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	2289	2660	gspI	0/0	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	1687	2256	gspJ	0/0	100.0	96.3	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	713	1690	gspK	0/0	100.0	96.4	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02408	93	480	gspM	0/0	91.7	93.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00409	826	1773	iucB	0/0	100.0	99.8	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig01249	221	974	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00071	894	3419	yagX/ecpC	0/0	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00071	200	868	yagY/ecpB	0/0	100.0	98.2	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01551	34	937	ybtA	0/0	94.2	99.7	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00307	530	2332	ybtQ	0/0	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00248	1616	2920	ybtS	0/0	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00842	524	1602	ybtU	0/0	98.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

Home-HIM_073B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00563	180	1607	aslA	2/2	99.9	96.3	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00102	1283	2311	chuS	0/0	100.0	97.7	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00277	1672	2466	chuV	0/0	99.2	99.5	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00720	731	1225	chuX	0/0	100.0	97.4	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00076	1833	3020	entC	0/0	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00076	700	1656	fepB	0/0	100.0	98.1	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00431	759	1574	fepC	0/0	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00861	115	570	gspG	0/0	100.0	94.5	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00861	607	1137	gspH	0/0	100.0	94.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00861	1134	1479	gspI	0/0	93.0	91.3	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00910	333	1310	gspK	0/0	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00571	1	1713	iucA	0/0	96.1	99.9	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00267	500	1837	iucD	0/0	100.0	99.8	NP_709457	(iucD) aerobactin synthesis protein IucC lysine 6-monooxygenase [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00087	1	1560	kpsD	0/0	93.0	99.0	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00527	683	1459	kpsM	0/0	100.0	99.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00527	27	686	kpsT	0/0	100.0	100.0	AAA24047	(kpsT) KpsT [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00868	3	1055	ompA	1/12	100.0	95.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00017	338	2860	papC	0/0	100.0	99.7	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00017	3060	3665	papD	0/0	100.0	99.7	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00017	4838	5377	papE	2/6	99.4	93.5	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00017	5422	5955	papF	1/3	100.0	94.0	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00856	508	1486	papG	0/0	96.8	99.2	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00017	3702	4283	papJ	0/0	100.0	97.9	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00017	4290	4829	papK	0/0	100.0	99.3	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00009	5505	6643	senB	0/0	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig01458	221	974	yagV/ecpE	0/0	99.7	97.6	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00173	382	1050	yagY/ecpB	0/0	100.0	98.8	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00773	659	1564	ybtA	0/0	94.4	99.7	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig01894	3	553	ykgK/ecpR	0/0	93.2	99.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_075A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00085	10279	11025	entA	0/0	100.0	95.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	9422	10279	entB	0/0	100.0	97.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	6601	7788	entC	0/0	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	7798	9408	entE	0/0	100.0	95.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00205	3936	7789	entF	0/0	99.3	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	4214	5464	entS	0/0	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00038	1157	3025	espL1	2/30	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	9064	13289	fdeC	1/3	99.4	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00205	33	2273	fepA	0/0	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	5468	6424	fepB	0/0	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	1298	2113	fepC	0/0	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	3099	4115	fepD	0/0	100.0	95.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	2110	3102	fepG	0/0	100.0	94.6	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00205	2516	3718	fes	0/0	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00697	1	603	fimA	1/1	99.5	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00699	220	822	fimB	0/0	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00284	4731	5456	fimC	0/0	100.0	97.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00284	2028	4664	fimD	0/0	100.0	98.7	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00284	1488	2021	fimF	0/0	100.0	96.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00284	972	1475	fimG	0/0	100.0	97.6	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00284	50	961	fimH	0/0	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00104	9605	10435	gspC	0/0	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	7515	9365	gspD	1/15	100.0	97.2	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	6022	7515	gspE	0/0	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	4823	6022	gspF	0/0	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	4327	4782	gspG	0/0	100.0	95.4	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	3760	4290	gspH	0/0	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	3392	3763	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	2790	3359	gspJ	0/0	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	1816	2793	gspK	0/0	100.0	97.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	641	1501	gspL	0/0	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00104	103	525	gspM	0/0	100.0	93.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	5511	6551	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	22395	23148	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	20828	22471	yagW/ecpD	0/0	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	18313	20838	yagX/ecpC	0/0	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	17619	18287	yagY/ecpB	0/0	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	16974	17561	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	16309	16899	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-HIM_82A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00144	3019	3765	entA	0/0	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00144	2162	3019	entB	0/0	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00144	538	2148	entE	0/0	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00267	133	702	espY2	0/0	100.0	93.3	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00446	1178	2194	fepD	0/0	100.0	96.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00446	2191	3149	fepG	0/0	96.6	93.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01087	791	1362	fimB	0/0	94.9	97.5	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00215	2055	4691	fimD	0/0	100.0	97.7	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01470	39	635	fimE	0/0	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00215	1515	2048	fimF	0/0	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00215	999	1502	fimG	0/0	100.0	97.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00215	77	988	fimH	0/0	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00751	675	1214	fimI	0/0	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00190	951	2801	gspD	1/15	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00190	2801	4294	gspE	0/0	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00351	2897	3352	gspG	0/0	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00351	2330	2860	gspH	0/0	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00351	1962	2333	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00351	1360	1929	gspJ	0/0	100.0	96.5	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00351	386	1363	gspK	0/0	100.0	96.9	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00202	822	1244	gspM	0/0	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00148	768	1715	iucB	0/0	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00148	1715	3457	iucC	0/0	100.0	99.7	NP_709456	(iucC) aerobactin synthesis protein IucC [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00148	3454	4791	iucD	0/0	100.0	99.5	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00041	3577	4617	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00195	119	4237	pic	0/0	100.0	100.0	YP_006098864	(pic) Pic serine protease precursor autotransporter [Pic (VF0218)] [Escherichia coli O44:H18 042]
contig00127	3678	4431	yagV/ecpE	0/0	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00127	2111	3754	yagW/ecpD	0/0	100.0	99.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01325	165	752	yagZ/ecpA	0/0	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00219	2862	3821	ybtA	0/0	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00219	893	2695	ybtP	0/0	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00299	1353	2657	ybtS	0/0	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00405	536	1339	ybtT	0/0	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00405	1336	2436	ybtU	0/0	100.0	99.9	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00299	2685	3965	ybtX	0/0	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

Home-KAT_009A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00903	81	1509	aslA	1/1	100.0	97.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00133	1290	2318	chuS	0/0	100.0	96.2	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00159	2421	3413	chuU	0/0	100.0	98.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00159	1654	2454	chuV	0/0	100.0	98.9	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00159	3462	4085	chuY	0/0	100.0	97.0	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00561	103	849	entA	0/0	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00314	1	1147	entC	0/0	96.5	96.8	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00314	1157	2767	entE	0/0	100.0	96.6	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00263	1124	2374	entS	0/0	100.0	95.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00263	164	1120	fepB	0/0	100.0	97.9	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00263	2473	3489	fepD	0/0	100.0	96.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01787	247	818	fimB	0/0	94.9	98.1	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00815	202	927	fimC	0/0	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00250	1280	3698	fimD	0/0	91.7	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00250	740	1273	fimF	0/0	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00250	224	727	fimG	0/0	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00815	964	1503	fimI	0/0	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00618	737	1596	gspL	1/1	99.9	94.7	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00618	200	621	gspM	0/0	99.8	92.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00123	2792	3955	iroB	0/0	100.0	98.7	NP_753168	(iroB) glucosyltransferase IroB [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00164	960	1916	iroE	0/0	100.0	99.5	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00164	1961	4138	iroN	0/0	100.0	98.9	NP_753164	(iroN) salmochelin receptor IroN [IroN (VF0230)] [Escherichia coli CFT073]
contig00286	975	1922	iucB	0/0	100.0	100.0	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00286	1922	3504	iucC	0/0	90.8	100.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00219	86	1423	iucD	0/0	100.0	100.0	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00219	1345	3624	iutA	0/0	100.0	100.0	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00097	2448	4124	kpsD	0/0	100.0	98.8	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00927	572	1348	kpsM	0/0	100.0	91.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00138	3117	4157	ompA	0/0	100.0	99.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00218	179	2701	papC	0/0	100.0	99.7	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00218	2901	3506	papD	0/0	100.0	100.0	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01112	46	1056	papG	0/0	100.0	98.8	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00386	63	296	papI	0/0	100.0	99.1	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01942	197	715	papK	0/0	96.1	99.2	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01767	196	747	papX	0/0	100.0	100.0	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00133	2367	4349	shuA	0/0	100.0	98.1	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00351	87	840	yagV/ecpE	0/0	99.7	97.2	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00328	1356	2024	yagY/ecpB	0/0	100.0	98.4	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00328	711	1298	yagZ/ecpA	0/0	100.0	98.8	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00153	733	2535	ybtQ	0/0	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00476	963	1766	ybtT	0/0	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00153	2528	3808	ybtX	0/0	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00328	46	636	ykgK/ecpR	0/0	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-KAT_013A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00416	470	1216	entA	0/0	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00275	271	2511	fepA	0/0	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00662	493	1308	fepC	0/0	100.0	97.4	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00915	434	1346	fimH	1/1	100.0	96.9	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00325	1579	2370	gspC	0/0	95.3	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00166	211	2061	gspD	1/15	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00775	400	930	gspH	0/0	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00775	927	1298	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00649	71	931	gspL	0/0	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00132	821	2563	iucC	0/0	100.0	98.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00482	581	1621	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00151	2534	3067	papF	1/3	100.0	94.0	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig02450	206	439	papI	0/0	100.0	95.3	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01902	91	759	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-KAT_023A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00085	3574	4246	entA	0/0	90.1	95.2	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	2717	3574	entB	0/0	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	1	1083	entC	0/0	91.2	97.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00085	1093	2703	entE	0/0	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00218	681	1697	fepD	0/0	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00218	1694	2686	fepG	0/0	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01999	64	669	fimA	0/0	100.0	90.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00173	1488	2021	fimF	0/0	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00173	972	1475	fimG	0/0	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00173	50	961	fimH	0/0	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00775	398	1355	iroE	1/1	100.0	98.8	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00009	748	1695	iucB	0/0	100.0	99.9	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00009	1695	3437	iucC	0/0	100.0	99.9	NP_709456	(iucC) aerobactin synthesis protein IucC [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00009	3434	4771	iucD	0/0	100.0	99.8	NP_709457	(iucD) aerobactin synthesis protein IucC lysine 6-monooxygenase [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00009	4693	6972	iutA	0/0	100.0	99.5	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig01264	158	1210	ompA	1/12	100.0	94.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00713	2	1627	yagW/ecpD	0/0	98.9	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01155	32	700	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig02000	115	702	yagZ/ecpA	0/0	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Home-KAT_039B

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00137	777	1769	fepG	0/0	100	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]

Hosp-BWE_048

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00952	305	1030	fimC	0/0	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	1082	1615	fimF	0/0	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	566	1069	fimG	0/0	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00299	445	1782	iucD	0/0	100.0	99.9	NP_709457	(iucD) aerobactin synthesis protein IucC lysine 6-monooxygenase [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00373	221	974	yagV/ecpE	0/0	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00372	510	1790	ybtX	0/0	100.0	99.4	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

Hosp-BWE_054

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00379	2508	3936	aslA	1/1	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00262	3105	5051	chuA	0/0	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00262	2028	3056	chuS	0/0	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00643	545	1537	chuT	0/0	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00193	3614	4606	chuU	0/0	100.0	99.2	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00193	2847	3647	chuV	0/0	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00193	5278	5772	chuX	0/0	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00193	4655	5278	chuY	0/0	100.0	98.4	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00720	382	609	daaF	0/0	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00722	1706	2149	draD	0/0	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00722	408	967	draE2	1/1	99.6	99.6	AAB65153	(draE2) Dr-II structural adhesin precursor [Afa/Dr family (VF0212)] [Escherichia coli EC7372]
contig00722	1154	1327	draP	0/0	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00076	8289	9035	entA	0/0	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00512	1009	2619	entE	0/0	100.0	99.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00393	1233	2483	entS	0/0	100.0	98.2	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00690	127	2367	fepA	0/0	100.0	98.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00393	273	1229	fepB	0/0	100.0	99.7	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00639	1325	2140	fepC	0/0	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00393	2582	3598	fepD	0/0	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00149	6124	6728	fimA	1/1	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00655	1007	1609	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00149	4758	5483	fimC	0/0	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00149	2055	4691	fimD	0/0	100.0	98.9	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00149	1515	2048	fimF	0/0	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00149	999	1502	fimG	0/0	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00149	77	988	fimH	0/0	100.0	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00149	5520	6059	fimI	0/0	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00668	710	2519	gspD	1/15	97.8	96.2	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00265	1233	2432	gspF	0/0	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00265	2473	2928	gspG	0/0	100.0	95.8	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00265	2965	3495	gspH	0/0	100.0	96.6	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00265	3492	3863	gspI	0/0	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00265	3896	4465	gspJ	0/0	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00675	551	1411	gspL	0/0	100.0	93.3	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00675	1527	1936	gspM	0/0	96.9	93.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00100	4056	5732	kpsD	0/0	100.0	99.5	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00792	431	1207	kpsM	0/0	100.0	91.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00036	1771	2823	ompA	1/12	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig01432	261	574	papB	1/1	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01348	282	515	papI	0/0	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01080	254	805	papX	0/0	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00111	6081	7219	senB	0/0	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00282	2077	2830	yagV/ecpE	0/0	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00282	510	2153	yagW/ecpD	0/0	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00132	4797	5465	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00132	4153	4740	yagZ/ecpA	0/0	100.0	98.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01009	336	1295	ybtA	0/0	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00225	3250	5052	ybtQ	0/0	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00225	645	1949	ybtS	0/0	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00329	3381	4184	ybtT	0/0	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00329	2284	3384	ybtU	0/0	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00225	1977	3257	ybtX	0/0	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00132	3488	4078	ykgK/ecpR	0/0	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-BWE_076

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00009	4506	4622	astA	0/0	100.0	99.1	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00742	341	1087	entA	0/0	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00542	3	1304	espX1	0/0	91.6	93.0	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01182	1	951	fepB	0/0	99.4	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00313	996	1598	fimB	0/0	100.0	97.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00126	167	700	fimF	0/0	100.0	96.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00814	285	1196	fimH	0/0	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00102	1	1254	ybtS	0/0	96.1	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00102	1282	2527	ybtX	0/0	97.3	99.4	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

Hosp-BWE_106

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00076	1638	2420	chuV	0/0	97.8	98.2	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00441	204	1385	fes	0/0	98.2	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00324	851	1456	fimA	0/0	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01983	13	615	fimB	0/0	100.0	99.5	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01193	12	515	fimG	0/0	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00324	247	786	fimI	0/0	100.0	99.4	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01866	1	549	gspJ	0/0	96.3	94.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig03019	2	423	gspM	0/0	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	1	1747	iucA	0/0	97.7	94.1	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00002	1748	2695	iucB	0/0	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00002	2695	4437	iucC	0/0	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00724	158	1134	ompA	1/12	92.7	95.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00436	157	1149	shuT	0/0	100.0	98.1	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00382	176	929	yagV/ecpE	0/0	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-HIM_031

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01444	115	861	entA	0/0	100	95.5	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig02230	18	614	fimE	0/0	100	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00717	912	1445	fimF	0/0	100	98.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00717	396	899	fimG	0/0	100	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00647	417	956	fimI	0/0	100	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00642	663	1493	gspC	0/0	100	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00300	1064	1519	gspG	0/0	100	95.8	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00300	1556	2086	gspH	0/0	100	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01153	393	962	gspJ	0/0	100	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00613	436	858	gspM	0/0	100	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00232	558	1226	yagY/ecpB	0/0	100	98.2	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01676	186	776	ykgK/ecpR	0/0	100	97.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-HIM_045

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00822	226	1654	aslA	1/1	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig01052	243	1430	entC	0/0	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01015	1	1505	entE	0/0	93.4	95.3	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00627	125	2365	fepA	0/0	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01175	235	1191	fepB	0/0	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00619	1318	2133	fepC	0/0	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00619	329	1321	fepG	0/0	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00328	1	1191	fes	0/0	99.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig01253	428	1033	fimA	0/0	100.0	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01421	252	854	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00382	2520	3245	fimC	0/0	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00382	1	2453	fimD	0/0	93.0	98.2	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01386	124	720	fimE	0/0	100.0	99.0	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00729	1488	2021	fimF	0/0	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00729	972	1475	fimG	0/0	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00729	50	961	fimH	0/0	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00629	1015	2055	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

Hosp-HIM_048

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00505	1198	1802	fimA	1/1	99.8	91.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00787	864	1466	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01204	215	940	fimC	0/0	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00089	1642	4077	fimD	0/0	92.4	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00505	178	774	fimE	0/0	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00089	1101	1634	fimF	0/0	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00089	585	1088	fimG	0/0	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00131	1166	2659	gspE	0/0	100.0	95.6	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00439	142	1119	gspK	0/0	100.0	96.9	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01240	716	1137	gspM	0/0	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00252	1	2066	hlyB	0/0	97.3	99.5	NP_755448	(hlyB) Hemolysin B [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00637	468	1805	iucD	0/0	100.0	100.0	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00668	295	1071	kpsM	0/0	100.0	95.2	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00306	15	1067	ompA	1/12	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig02167	255	567	papB	0/0	99.4	99.7		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	644	3166	papC	0/0	100.0	99.8	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	3366	3971	papD	0/0	100.0	100.0	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	5734	6264	papF	0/0	100.0	99.2	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	6308	7318	papG	0/0	100.0	99.4	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	10	597	papH	0/0	100.0	98.6	NP_755466	(papH) P pilus termination subunit PapH [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	4008	4589	papJ	0/0	100.0	98.3	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	4596	5135	papK	0/0	100.0	99.4	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01881	196	747	papX	0/0	100.0	100.0	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00027	692	4591	sat	0/0	100.0	100.0	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00018	4535	5673	senB	0/0	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig01241	268	1021	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00046	3537	4124	yagZ/ecpA	0/0	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01487	1	1023	ybtU	0/0	92.9	99.4	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00412	1061	2269	ybtX	0/0	94.4	97.4	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00046	2872	3462	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-HIM_068

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00394	1571	2317	entA	0/0	100.0	95.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00394	714	1571	entB	0/0	100.0	97.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00534	254	1441	entC	0/0	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00059	3826	7679	entF	0/0	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00059	11969	13219	entS	0/0	100.0	95.5	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00035	5891	7759	espL1	2/30	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00046	12749	14041	espX5	0/0	100.0	95.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00059	1	2163	fepA	0/0	96.5	97.1	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00059	13223	14179	fepB	0/0	100.0	97.3	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00059	9053	9868	fepC	0/0	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00059	10854	11870	fepD	0/0	100.0	95.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00059	9865	10857	fepG	0/0	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00059	2406	3608	fes	0/0	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00348	3818	4422	fimA	1/1	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00584	1002	1604	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00348	2452	3177	fimC	0/0	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00348	1	2385	fimD	0/0	90.4	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00752	15	611	fimE	0/0	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00535	1500	2033	fimF	0/0	100.0	98.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00535	984	1487	fimG	0/0	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00535	62	973	fimH	0/0	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00348	3214	3753	fimI	0/0	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00095	9605	10435	gspC	0/0	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	7515	9365	gspD	1/15	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	6022	7515	gspE	0/0	100.0	96.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	4823	6022	gspF	0/0	100.0	96.3	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	4327	4782	gspG	0/0	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	3760	4290	gspH	0/0	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	3392	3763	gspI	0/0	100.0	94.1	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	2790	3359	gspJ	0/0	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	1816	2793	gspK	0/0	100.0	97.3	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	641	1501	gspL	0/0	100.0	97.3	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00095	103	525	gspM	0/0	100.0	97.2	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00050	1576	2616	ompA	0/0	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00262	2424	3177	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00262	857	2500	yagW/ecpD	0/0	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00145	1290	1958	yagY/ecpB	0/0	100.0	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00145	2016	2599	yagZ/ecpA	0/0	99.3	99.1	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00145	2677	3267	ykgK/ecpR	0/0	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-HIM_071A

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00768	67	1494	aslA	2/2	99.9	96.3	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00126	2670	3662	chuU	0/0	100.0	99.2	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00126	154	1491	chuW	0/0	100.0	98.6	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00126	1504	1998	chuX	0/0	100.0	97.4	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00126	1998	2621	chuY	0/0	100.0	98.6	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig01198	123	1277	entC	0/0	97.2	97.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00471	1	1583	entE	0/0	98.3	98.3	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00553	834	1403	espY2	0/0	100.0	94.2	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00181	793	1608	fepC	0/0	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00181	1605	2597	fepG	0/0	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00917	258	1460	fes	0/0	100.0	97.4	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00355	1174	2588	gspE	0/0	94.7	94.3	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00288	1655	2830	gspF	0/0	98.0	94.3	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00288	1159	1614	gspG	0/0	100.0	94.5	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00288	592	1122	gspH	0/0	100.0	94.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00288	224	595	gspI	0/0	100.0	91.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01201	181	1158	gspK	0/0	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00641	110	970	gspL	0/0	100.0	94.9	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00641	1086	1507	gspM	0/0	99.8	93.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00472	1	2084	iutA	0/0	94.9	99.9	NP_709458	(iutA) aerobactin receptor IutA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00945	323	1099	kpsM	0/0	100.0	99.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00011	260	2782	papC	0/0	100.0	99.7	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	2982	3587	papD	0/0	100.0	99.7	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	4760	5299	papE	2/6	99.4	93.5	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	5344	5877	papF	1/3	100.0	94.0	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	5921	6931	papG	0/0	100.0	99.0	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	3624	4205	papJ	0/0	100.0	97.9	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00011	4212	4751	papK	0/0	100.0	99.3	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00979	355	906	papX	0/0	100.0	97.8	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00127	2331	3469	senB	0/0	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00231	1338	2006	yagY/ecpB	0/0	100.0	98.8	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00231	693	1280	yagZ/ecpA	0/0	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	4148	4951	ybtT	0/0	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00040	3051	4151	ybtU	0/0	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00682	410	1690	ybtX	0/0	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00231	28	618	ykgK/ecpR	0/0	100.0	99.7	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-HIM_82

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig02589	186	374	afaF-VII	0/0	100	98.4	AAK16195	(afaF-VII) AfaF-VII [Afimbrial adhesin AfaE-VIII (AI015)] [Escherichia coli str. 239 KH 89]
contig00475	115	861	entA	0/0	100	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01584	342	875	fimF	0/0	100	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00132	1032	1487	gspG	0/0	100	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00132	1524	2054	gspH	0/0	100	95.3	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00132	2051	2422	gspI	0/0	100	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00132	2455	3024	gspJ	0/0	100	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00387	514	1851	iucD	0/0	100	100.0	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00303	537	1577	ompA	0/0	100	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig01105	853	1122	stx1B	0/0	100	100.0	NP_288672	(stx1B) shiga-like toxin 1 subunit B encoded within prophage CP-933V [Stx (VF0206)] [Escherichia coli O157:H7 str. EDL933]

Hosp-KAT_009

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00437	285	1313	chuS	0/0	100.0	96.9	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00284	219	995	eltA	0/0	100.0	98.8	AAA24685	(eltA) heat-labile enterotoxin A prepeptide (from human) [Heat-labile toxin (LT) (VF0210)] [Escherichia coli]
contig00284	992	1366	eltB	0/0	100.0	99.2	AAA98064	(eltB) enterotoxin subunit B (from human) [Heat-labile toxin (LT) (VF0210)] [Escherichia coli]
contig00436	1605	2291	entA	0/0	92.0	94.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00436	748	1603	entB	0/0	99.8	95.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00979	57	1244	entC	0/0	100.0	95.8	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	1	4169	fdeC	1/3	98.1	92.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00459	1112	1927	fepC	0/0	100.0	96.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00478	632	1648	fepD	0/0	100.0	96.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00937	369	1486	fes	0/0	92.9	96.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig02014	188	732	fimB	0/0	90.4	96.9	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01335	299	1024	fimC	0/0	100.0	96.7	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01457	219	752	fimF	0/0	100.0	96.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00681	332	1162	gspC	0/0	100.0	94.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00922	30	560	gspH	0/0	100.0	94.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00922	557	928	gspI	0/0	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00922	961	1500	gspJ	0/0	94.7	94.3	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01426	142	560	gspM	0/0	99.0	93.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00240	1784	2824	ompA	0/0	100.0	98.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00735	400	1392	shuT	0/0	100.0	98.4	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig01417	305	1047	shuV	0/0	96.4	98.9	YP_405013	(shuV) ATP-binding component of hemin transport system [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig01321	305	973	yagY/ecpB	0/0	100.0	97.8	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-KAT_013

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00342	678	2106	aslA	1/1	100.0	97.3	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00416	998	1813	fepC	0/0	100.0	96.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01042	156	1285	fes	0/0	93.9	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00077	1497	2030	fimF	0/0	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00077	981	1484	fimG	0/0	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00077	59	970	fimH	0/0	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00227	331	1530	gspF	0/0	100.0	94.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00227	1571	2026	gspG	0/0	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00227	2063	2593	gspH	0/0	100.0	95.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	6001	6754	yagV/ecpE	0/0	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	4434	6077	yagW/ecpD	0/0	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	1919	4444	yagX/ecpC	0/0	100.0	99.0	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	1225	1893	yagY/ecpB	0/0	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	584	1167	yagZ/ecpA	0/0	99.3	99.1	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-KAT_023

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00843	1	1365	aslA	1/1	95.5	97.4	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00283	1046	2074	chuS	0/0	100.0	96.2	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00065	3431	4423	chuU	0/0	100.0	98.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00065	915	2252	chuW	0/0	100.0	96.7	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00065	2759	3382	chuY	0/0	100.0	97.0	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig01490	509	736	daaF	0/0	100.0	98.7	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig02616	190	495	draA	0/0	100.0	100.0	AAK16475	(draA) cytoplamic protein DraA [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00872	709	1453	draB	1/1	100.0	99.9	AAK16476	(draB) chaperone protein DraB [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig01310	299	472	draP	0/0	100.0	98.3	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00133	1	3563	entF	0/0	91.8	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00156	815	2065	entS	0/0	100.0	95.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00633	546	1361	fepC	0/0	100.0	96.8	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00156	2164	3180	fepD	0/0	100.0	96.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00627	1	559	fimA	0/0	92.2	90.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01719	254	856	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00627	1200	1900	fimC	0/0	96.6	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	2049	4685	fimD	0/0	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	1509	2042	fimF	0/0	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	993	1496	fimG	0/0	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	71	982	fimH	0/0	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00627	624	1163	fimI	0/0	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00983	619	990	gspI	0/0	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00983	17	586	gspJ	0/0	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02492	200	588	gspM	0/0	92.0	93.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00060	905	2226	iucD	1/1	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00931	540	1316	kpsM	0/0	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig01543	747	1031	papB	1/1	90.5	98.2		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig02677	222	455	papI	0/0	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00065	1	895	shuT	0/0	90.1	98.2	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00065	2265	2759	shuX	0/0	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00025	3022	3775	yagV/ecpE	0/0	99.7	97.2	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	1455	3098	yagW/ecpD	0/0	100.0	99.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00244	2114	2782	yagY/ecpB	0/0	100.0	98.4	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00244	1469	2056	yagZ/ecpA	0/0	100.0	98.8	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00189	1388	2965	ybtE	0/0	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00189	581	1384	ybtT	0/0	100.0	99.2	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00244	804	1394	ykgK/ecpR	0/0	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

Hosp-KAT_039

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00974	316	1173	entB	0/0	100.0	97.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00753	97	1347	entS	0/0	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00093	1084	2982	espL1	0/0	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00468	1485	2300	fepC	0/0	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00468	496	1488	fepG	0/0	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00550	931	2133	fes	0/0	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig01098	744	1346	fimB	0/0	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00242	1704	2429	fimC	0/0	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	3858	4391	fimF	0/0	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	3342	3845	fimG	0/0	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00060	2420	3331	fimH	0/0	100.0	97.8	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00242	2466	3005	fimI	0/0	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00965	151	522	gspI	0/0	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00965	555	1124	gspJ	0/0	100.0	97.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01628	222	644	gspM	0/0	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00282	221	974	yagV/ecpE	0/0	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00218	1	2322	yagX/ecpC	0/0	91.9	98.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01086	564	1232	yagY/ecpB	0/0	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00260	2553	3143	ykgK/ecpR	0/0	100.0	97.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

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Multi-Locus Sequence Typing (MLST)

Symbol	Meaning
~	novel full length allele similar to match
?	partial match to known allele
-	allele missing

	Scheme	ST	1	2	3	4	5	6	7
Catt-BWE_048B	ecoli	-	adk(-)	fumC(1489?)	gyrB(14)	icd(16)	mdh(948?)	purA(8)	recA(14)
Catt-BWE_054A	ecoli	-	adk(18)	fumC(1238)	gyrB(764)	icd(1197?)	mdh(4)	purA(5)	recA(4)
Catt-BWE_113B	ecoli	-	adk(6)	fumC(6)	gyrB(3)	icd(1149?)	mdh(7)	purA(7)	recA(6)
Catt-HIM_031B	-	-
Catt-HIM_045B	ecoli	-	adk(6)	fumC(-)	gyrB(983?)	icd(1158?)	mdh(866?)	purA(2)	recA(779?)
Catt-HIM_048B	senterica	-	aroC(621)	dnaN(559)	hemD(496?)	hisD(764?)	purE(617)	sucA(281)	thrA(695)
Catt-HIM_068A	ecoli	-	adk(9)	fumC(65)	gyrB(5)	icd(1249?)	mdh(9)	purA(13)	recA(6)
Catt-HIM_073A	ecoli	-	adk(-)	fumC(1431?)	gyrB(3)	icd(1232?)	mdh(11)	purA(8)	recA(6)
Catt-HIM_082A1	ecoli	-	adk(9)	fumC(-)	gyrB(5)	icd(1247?)	mdh(9)	purA(13)	recA(6)
Catt-KAT_009_A1	ecoli	10	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
Catt-KAT_013A1	ecoli	-	adk(1050?)	fumC(19)	gyrB(33)	icd(1232?)	mdh(11)	purA(8)	recA(6)
Catt-KAT_036B	-	-
Home-BWE_054A	ecoli	2	adk(5)	fumC(3)	gyrB(2)	icd(6)	mdh(5)	purA(5)	recA(4)
Home-HIM_031A	ecoli	-	adk(842?)	fumC(1518?)	gyrB(32)	icd(16)	mdh(11)	purA(8)	recA(14)
Home-HIM_032A	ecoli	-	adk(10)	fumC(1521?)	gyrB(5)	icd(364?)	mdh(949?)	purA(8)	recA(780?)
Home-HIM_045A	ecoli	-	adk(6)	fumC(4)	gyrB(14)	icd(1166?)	mdh(24)	purA(8)	recA(14)
Home-HIM_047B	ecloacae	-	dnaA(~93)	fusA(18)	gyrB(~276)	leuS(107)	pyrG(34)	rplB(110)	rpoB(29)
Home-HIM_048A	ecoli	-	adk(13)	fumC(888?)	gyrB(10)	icd(97)	mdh(17)	purA(94)	recA(93)
Home-HIM_068B	cfreundii	-	aspC(171)	clpX(193?)	fadD(112?)	mdh(172)	arcA(~114)	dnaG(84)	lysP(-)
Home-HIM_071A	ecoli	-	adk(351)	fumC(1467?)	gyrB(54)	icd(54)	mdh(1)	purA(35)	recA(151)
Home-HIM_072A	senterica	-	aroC(~622)	dnaN(559)	hemD(552)	hisD(765?)	purE(~690)	sucA(~580)	thrA(695)
Home-HIM_073B	ecoli	-	adk(27)	fumC(-)	gyrB(24)	icd(-)	mdh(26)	purA(168?)	recA(745?)
Home-HIM_075A	ecoli	-	adk(1081?)	fumC(579)	gyrB(3)	icd(16)	mdh(11)	purA(8)	recA(6)
Home-HIM_82A	ecoli	-	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(949?)	purA(8)	recA(2)
Home-KAT_009A	ecoli	-	adk(21)	fumC(1394?)	gyrB(946?)	icd(6)	mdh(5)	purA(5)	recA(725?)
Home-KAT_013A	senterica	-	aroC(621)	dnaN(559)	hemD(~496)	hisD(-)	purE(617)	sucA(281?)	thrA(~633)
Home-KAT_023A	ecoli	10	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
Home-KAT_039B	ecoli	-	adk(-)	fumC(11)	gyrB(983?)	icd(1250?)	mdh(915?)	purA(8)	recA(2)
Hosp-BWE_048	ecoli	-	adk(10)	fumC(1521?)	gyrB(979?)	icd(1250?)	mdh(923?)	purA(8)	recA(776?)
Hosp-BWE_054	ecoli	-	adk(53)	fumC(40)	gyrB(945?)	icd(13)	mdh(36)	purA(28)	recA(29)
Hosp-BWE_076	ecoli	-	adk(670?)	fumC(1487?)	gyrB(983?)	icd(-)	mdh(923?)	purA(8)	recA(2)
Hosp-BWE_106	-	-
Hosp-HIM_031	senterica	-	aroC(622?)	dnaN(559)	hemD(343?)	hisD(~763)	purE(~686)	sucA(~580)	thrA(~695)
Hosp-HIM_045	senterica	-	aroC(621)	dnaN(559)	hemD(496)	hisD(764?)	purE(617)	sucA(281)	thrA(~695)
Hosp-HIM_048	ecoli	-	adk(6)	fumC(4)	gyrB(983?)	icd(1149?)	mdh(24)	purA(8)	recA(14)
Hosp-HIM_068	ecoli	-	adk(6)	fumC(23?)	gyrB(15)	icd(26)	mdh(9)	purA(8)	recA(7)
Hosp-HIM_071A	ecoli	-	adk(27)	fumC(32?)	gyrB(24)	icd(29)	mdh(944?)	purA(19)	recA(22)
Hosp-HIM_82	ecoli	-	adk(10)	fumC(-)	gyrB(4)	icd(8)	mdh(775?)	purA(35)	recA(766?)
Hosp-KAT_009	ecoli	-	adk(52)	fumC(403)	gyrB(76?)	icd(761?)	mdh(902?)	purA(40)	recA(278)
Hosp-KAT_013	senterica	-	aroC(622?)	dnaN(559?)	hemD(496)	hisD(764?)	purE(~690)	sucA(281?)	thrA(695?)
Hosp-KAT_023	cfreundii	-	aspC(69)	clpX(169?)	fadD(77)	mdh(175?)	arcA(~111)	dnaG(164?)	lysP(~101)
Hosp-KAT_039	ecoli	-	adk(6)	fumC(6)	gyrB(33)	icd(1232?)	mdh(11)	purA(8)	recA(2)

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Pangenome Analysis

Pangenome genes summary

Genes	Description	Number
Core genes	(99% <= strains <= 100%)	0
Soft core genes	(95% <= strains < 99%)	27
Shell genes	(15% <= strains < 95%)	5645
Cloud genes	(0% <= strains < 15%)	17237
Total genes	(0% <= strains <= 100%)	22909

Schematic representation of genes presence (color) or absence (blank) between samples:

Pangenome tree based on presence/absence of accesory genes representation

Rectangular (phylogram)

Circular (phylogram)

Rectangular (cladogram)

Circular (cladogram)

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Pangenome tree based on core genome alignment representation

Rectangular (phylogram)

Circular (phylogram)

Rectangular (cladogram)

Circular (cladogram)

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